scanpy_plot: plot.xml annotate

author	iuc
date	Mon, 04 Mar 2019 10:09:58 -0500
parents
children	072b759d0fca

rev	line source
0 729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1 <tool id="scanpy_plot" name="Plot with scanpy" version="@galaxy_version@">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2 <description></description>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	3 <macros>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	4 <import>macros.xml</import>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	5 </macros>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	6 <expand macro="requirements"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	7 <stdio>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	8 <regex match="... storing" source="stderr" level="warning"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	9 </stdio>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	10 <expand macro="version_command"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	11 <command detect_errors="exit_code"><![CDATA[
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	12 @CMD@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	13 ]]></command>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	14 <configfiles>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	15 <configfile name="script_file"><![CDATA[
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	16 @CMD_imports@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	17 @CMD_read_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	18
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	19 sc.settings.figdir = '.'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	20
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	21 #if $method.method == 'pl.scatter'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	22
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	23 sc.pl.scatter(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	24 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	25 #if $method.type.type == 'xy'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	26 x='$method.type.x',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	27 y='$method.type.y',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	28 layers=('$method.type.layer_x', '$method.type.layer_y', '$method.type.layer_color'),
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	29 #else
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	30 basis='$method.type.basis',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	31 #if str($method.type.color) != ''
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	32 #set $color = ([x.strip() for x in str($method.type.color).split(',')])
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	33 color=$color,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	34 #else
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	35 color=None,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	36 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	37 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	38 use_raw=$method.use_raw,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	39 sort_order=$method.sort_order,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	40 @CMD_params_pl_groups@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	41 @CMD_params_pl_components@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	42 projection='$method.plot.projection',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	43 legend_loc='$method.plot.legend_loc',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	44 legend_fontsize=$method.plot.legend_fontsize,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	45 legend_fontweight='$method.plot.legend_fontweight',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	46 color_map='$method.plot.color_map',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	47 palette='$method.plot.palette',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	48 frameon=$method.plot.frameon,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	49 #if $method.plot.title
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	50 title='$method.plot.title',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	51 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	52 size=$method.plot.size)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	53
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	54 #elif $method.method == 'pl.heatmap'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	55 sc.pl.heatmap(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	56 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	57 @CMD_params_plots@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	58 swap_axes=$method.swap_axes,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	59 show_gene_labels=$method.show_gene_labels,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	60 cmap='$method.matplotlib_pyplot_imshow.cmap',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	61 interpolation='$method.matplotlib_pyplot_imshow.interpolation',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	62 #if $method.matplotlib_pyplot_imshow.alpha
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	63 alpha=$method.matplotlib_pyplot_imshow.alpha,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	64 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	65 #if $method.matplotlib_pyplot_imshow.vmin
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	66 vmin=$method.matplotlib_pyplot_imshow.vmin,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	67 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	68 #if $method.matplotlib_pyplot_imshow.vmax
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	69 vmax=$method.matplotlib_pyplot_imshow.vmax,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	70 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	71 origin='$method.matplotlib_pyplot_imshow.origin')
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	72
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	73 #elif $method.method == 'pl.dotplot'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	74 sc.pl.dotplot(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	75 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	76 @CMD_params_plots@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	77 color_map='$method.color_map',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	78 #if $method.dot_max
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	79 dot_max=$method.dot_max,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	80 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	81 #if $method.dot_min
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	82 dot_min=$method.dot_min,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	83 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	84 @CMD_params_matplotlib_pyplot_scatter@)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	85
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	86 #elif $method.method == 'pl.violin'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	87 sc.pl.violin(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	88 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	89 #if $method.key_variables.type == "var_names"
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	90 #set $key_list = adata.var_names
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	91 #elif $method.key_variables.type == "obs"
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	92 #set $key_list = adata.obs.select_dtypes(exclude=['category']).columns
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	93 #elif $method.key_variables.type == "custom"
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	94 #set $key_list=([x.strip() for x in str($method.key_variables.keys).split(',')])
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	95 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	96 keys=$key_list,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	97 #if $method.groupby
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	98 groupby='$method.groupby',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	99 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	100 log=$method.log,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	101 use_raw=$method.use_raw,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	102 sstripplot=$method.violin_plot.stripplot.stripplot,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	103 #if $method.violin_plot.stripplot.stripplot == "True"
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	104 jitter=$method.violin_plot.stripplot.jitter.jitter,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	105 #if $method.violin_plot.stripplot.jitter.jitter == "True"
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	106 size=$method.violin_plot.stripplot.jitter.size,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	107 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	108 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	109 multi_panel=$method.violin_plot.multi_panel.multi_panel,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	110 scale='$method.violin_plot.scale',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	111 #if $method.xlabel
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	112 xlabel='$method.xlabel',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	113 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	114 #if $method.rotation
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	115 rotation=$method.rotation,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	116 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	117 @CMD_params_seaborn_violinplot@)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	118
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	119 #elif $method.method == 'pl.matrixplot'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	120 sc.pl.matrixplot(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	121 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	122 @CMD_params_plots@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	123 swap_axes=$method.swap_axes,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	124 cmap='$method.matplotlib_pyplot_pcolor.cmap',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	125 #if $method.matplotlib_pyplot_pcolor.vmin
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	126 vmin=$method.matplotlib_pyplot_pcolor.vmin,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	127 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	128 #if $method.matplotlib_pyplot_pcolor.vmax
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	129 vmax=$method.matplotlib_pyplot_pcolor.vmax,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	130 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	131 edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	132 #if $method.matplotlib_pyplot_pcolor.alpha
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	133 alpha=$method.matplotlib_pyplot_pcolor.alpha,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	134 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	135 snap=$method.matplotlib_pyplot_pcolor.snap)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	136
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	137 #elif $method.method == 'pl.clustermap'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	138 sc.pl.clustermap(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	139 #if str($method.use_raw) == 'True'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	140 adata=adata.X,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	141 #else
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	142 adata=adata,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	143 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	144 show=False,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	145 obs_keys='$method.obs_keys',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	146 use_raw=$method.use_raw,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	147 method='$method.seaborn_clustermap.method',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	148 metric='$method.seaborn_clustermap.metric',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	149 #if str($method.seaborn_clustermap.z_score) == 'None'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	150 z_score=None,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	151 #else
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	152 z_score=$method.seaborn_clustermap.z_score,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	153 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	154 #if str($method.seaborn_clustermap.standard_scale) == 'None'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	155 standard_scale=None,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	156 #else
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	157 standard_scale=$method.seaborn_clustermap.standard_scale,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	158 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	159 col_cluster=$method.seaborn_clustermap.col_cluster,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	160 row_cluster=$method.seaborn_clustermap.row_cluster).savefig(fname="output.$format")
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	161
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	162 #elif $method.method == 'pl.highest_expr_genes'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	163 sc.pl.highest_expr_genes(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	164 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	165 n_top=$method.n_top,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	166 #if str($method.gene_symbols) != ''
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	167 gene_symbols='$method.gene_symbols',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	168 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	169 #if str($method.setseaborn_boxplot.color) != ''
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	170 color='$method.setseaborn_boxplot.color',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	171 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	172 #if str($method.setseaborn_boxplot.palette) != 'None'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	173 palette='$method.setseaborn_boxplot.palette',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	174 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	175 saturation=$method.setseaborn_boxplot.saturation)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	176
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	177 #elif $method.method == 'pl.pca'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	178 sc.pl.pca(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	179 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	180 @CMD_param_color@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	181 use_raw=$method.use_raw,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	182 sort_order=$method.sort_order,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	183 @CMD_params_pl_groups@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	184 @CMD_params_pl_components@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	185 @CMD_pl_attribute_section@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	186 @CMD_params_matplotlib_pyplot_scatter@)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	187
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	188 #elif $method.method == 'pl.pca_loadings'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	189 sc.pl.pca_loadings(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	190 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	191 #set $components = ([int(x.strip()) for x in str($method.components).split(',')])
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	192 components=$components)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	193
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	194 #elif $method.method == 'pl.pca_variance_ratio'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	195 sc.pl.pca_variance_ratio(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	196 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	197 n_pcs=$method.n_pcs,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	198 log=$method.log)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	199
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	200 #elif $method.method == 'pl.pca_overview'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	201 sc.pl.pca_overview(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	202 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	203 @CMD_param_color@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	204 use_raw=$method.use_raw,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	205 sort_order=$method.sort_order,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	206 @CMD_params_pl_groups@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	207 @CMD_params_pl_components@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	208 @CMD_pl_attribute_section@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	209 @CMD_params_matplotlib_pyplot_scatter@)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	210
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	211 #elif $method.method == 'pl.tsne'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	212 sc.pl.tsne(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	213 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	214 @CMD_param_color@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	215 use_raw=$method.use_raw,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	216 @CMD_pl_edges@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	217 arrows=$method.arrows,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	218 sort_order=$method.sort_order,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	219 @CMD_params_pl_groups@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	220 @CMD_params_pl_components@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	221 @CMD_pl_attribute_section@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	222 @CMD_params_matplotlib_pyplot_scatter@)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	223
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	224 #elif $method.method == 'pl.umap'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	225 sc.pl.umap(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	226 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	227 @CMD_param_color@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	228 use_raw=$method.use_raw,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	229 @CMD_pl_edges@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	230 arrows=$method.arrows,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	231 sort_order=$method.sort_order,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	232 @CMD_params_pl_groups@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	233 @CMD_params_pl_components@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	234 @CMD_pl_attribute_section@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	235 @CMD_params_matplotlib_pyplot_scatter@)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	236
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	237 #elif $method.method == 'pl.diffmap'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	238 sc.pl.diffmap(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	239 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	240 @CMD_param_color@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	241 use_raw=$method.use_raw,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	242 sort_order=$method.sort_order,
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	243 @CMD_params_pl_groups@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	244 @CMD_params_pl_components@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	245 @CMD_pl_attribute_section@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	246 @CMD_params_matplotlib_pyplot_scatter@)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	247
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	248 #elif $method.method == 'pl.dpt_groups_pseudotime'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	249 sc.pl.dpt_groups_pseudotime(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	250 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	251 color_map='$method.color_map')
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	252
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	253 #elif $method.method == 'pl.dpt_timeseries'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	254 sc.pl.dpt_timeseries(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	255 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	256 #if $method.heatmap.as_heatmap == "True"
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	257 color_map='$method.heatmap.color_map',
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	258 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	259 as_heatmap=$method.heatmap.as_heatmap)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	260
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	261 #elif $method.method == 'pl.paga'
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	262 sc.pl.paga(
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	263 @CMD_param_plot_inputs@
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	264 @CMD_params_pl_paga@)
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	265 #end if
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	266 ]]></configfile>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	267 </configfiles>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	268 <inputs>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	269 <expand macro="inputs_anndata"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	270 <expand macro="param_plot_format"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	271 <conditional name="method">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	272 <param argument="method" type="select" label="Method used for plotting">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	273 <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using `pl.scatter`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	274 <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using `pl.heatmap`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	275 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using `pl.dotplot`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	276 <option value="pl.violin">Generic: Violin plot, using `pl.violin`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	277 <!--<option value="pl.stacked_violin">Generic: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	278 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using `pl.matrixplot`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	279 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using `pl.clustermap`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	280 <!--<option value="pl.ranking">Generic: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	281 <option value="pl.highest_expr_genes">Preprocessing: Plot the fraction of counts assigned to each gene over all cells, using `pl.highest_expr_genes`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	282 <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using `pl.filter_genes_dispersion`</option>-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	283 <!--<option value="pl.highly_variable_genes">Preprocessing: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	284 <!--<option value="pl.calculate_qc_metrics">Preprocessing: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	285 <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using `pl.pca`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	286 <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using `pl.pca_loadings`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	287 <option value="pl.pca_variance_ratio">PCA: Scatter plot in PCA coordinates, using `pl.pca_variance_ratio`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	288 <option value="pl.pca_overview">PCA: Plot PCA results, using `pl.pca_overview`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	289 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using `pl.tsne`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	290 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using `pl.umap`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	291 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using `pl.diffmap`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	292 <!--<option value="pl.draw_graph">Embeddings: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	293 <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using `pl.dpt_groups_pseudotime`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	294 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using `pl.dpt_timeseries`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	295 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using `pl.paga`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	296 <!--<option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	297 <!--<option value="pl.paga_path">Branching trajectories and pseudotime, clustering: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	298 <!--<option value="pl.rank_gene_groups">Marker genes: Plot ranking of genes using dotplot plot, using `pl.rank_gene_groups`</option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	299 <!--<option value="pl.rank_genes_groups_dotplot">Marker genes: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	300 <!--<option value="pl.rank_genes_groups_heatmap">Marker genes: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	301 <!--<option value="pl.rank_genes_groups_matrixplot">Marker genes: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	302 <!--<option value="pl.rank_genes_groups_stacked_violin">Marker genes: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	303 <!--<option value="pl.rank_genes_groups_violin">Marker genes: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	304 <!--<option value="pl.phate">Misc: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	305 <!--<option value="pl.matrix">Misc: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	306 <!--<option value="pl.paga_adjacency">Misc: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	307 <!--<option value="pl.timeseries">Misc: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	308 <!--<option value="pl.timeseries_as_heatmap">Misc: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	309 <!--<option value="pl.timeseries_subplot">Misc: </option>!-->
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	310 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	311 <when value="pl.scatter">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	312 <conditional name="type">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	313 <param name="type" type="select" label="Plotting tool that computed coordinates" help="">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	314 <option value="xy">Using coordinates</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	315 <option value="basis">Using tool that computes coordinates</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	316 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	317 <when value="xy">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	318 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either `.obs` or `.var`"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	319 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either `.obs` or `.var`"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	320 <param argument="layer_x" type="text" value="X" label="Layers for x coordinate" help="Use the `layers` attribute of `adata` if present"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	321 <param argument="layer_y" type="text" value="X" label="Layers for y coordinate" help="Use the `layers` attribute of `adata` if present"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	322 <param argument="layer_color" type="text" value="X" label="Layers for color" help="Use the `layers` attribute of `adata` if present"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	323 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	324 <when value="basis">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	325 <param argument="basis" type="select" label="Plotting tool that computes coordinates" help="">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	326 <option value="pca">pca (need to run on `tl.pca` output)</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	327 <option value="tsne">tsne (need to run on `tl.tsne` output)</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	328 <option value="umap">umap (need to run on `tl.umap` output)</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	329 <option value="diffmap">diffmap (need to run on `tl.diffmap` output)</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	330 <option value="draw_graph_fr">draw_graph_fr (need to run on `tl.draw_graph` output)</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	331 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	332 <expand macro="param_color"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	333 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	334 </conditional>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	335 <expand macro="param_use_raw"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	336 <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot data points with higher values on top of others?" help="For continuous annotations used as color parameter"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	337 <expand macro="pl_groups"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	338 <section name="plot" title="Plot attributes">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	339 <expand macro="pl_components"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	340 <expand macro="param_projection"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	341 <expand macro="param_legend_loc"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	342 <expand macro="param_legend_fontsize"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	343 <expand macro="param_legend_fontweight"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	344 <expand macro="param_color_map"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	345 <expand macro="param_palette"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	346 <expand macro="param_frameon"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	347 <expand macro="param_size"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	348 <expand macro="param_title"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	349 </section>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	350 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	351 <when value="pl.heatmap">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	352 <expand macro="params_plots"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	353 <expand macro="param_swap_axes"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	354 <param argument="show_gene_labels" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show gene labels?" help="By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed."/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	355 <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	356 <expand macro="param_cmap"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	357 <param name="interpolation" type="select" label="Interpolation method" help="">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	358 <option value="none">none</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	359 <option value="nearest">nearest</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	360 <option value="bilinear">bilinear</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	361 <option value="bicubic">bicubic</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	362 <option value="spline16">spline16</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	363 <option value="spline36">spline36</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	364 <option value="hanning">hanning</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	365 <option value="hamming">hamming</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	366 <option value="hermite">hermite</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	367 <option value="kaiser">kaiser</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	368 <option value="quadric">quadric</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	369 <option value="catrom">catrom</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	370 <option value="gaussian">gaussian</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	371 <option value="bessel">bessel</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	372 <option value="sinc">sinc</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	373 <option value="mitchell">mitchell</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	374 <option value="lanczos">lanczos</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	375 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	376 <expand macro="param_alpha"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	377 <expand macro="param_vmin"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	378 <expand macro="param_vmax"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	379 <param name="origin" type="select" label="Place the [0,0] index of the array in the upper left or lower left corner of the axes" help=" The convention 'upper' is typically used for matrices and images.">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	380 <option value="upper">Upper</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	381 <option value="lower">Lower</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	382 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	383 </section>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	384 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	385 <when value="pl.dotplot">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	386 <expand macro="params_plots"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	387 <param argument="color_map" type="select" label="Color palette">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	388 <expand macro="matplotlib_pyplot_colormap"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	389 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	390 <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	391 <param argument="dot_min" type="float" value="" min="0" max="1" optional="true" label="Minimum dot size" help="If none, the minimum dot size is set to 0. If given, the value should be a number between 0 and 1. All fractions smaller than dot_min are clipped to this value."/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	392 <expand macro="section_matplotlib_pyplot_scatter"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	393 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	394 <when value="pl.violin">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	395 <conditional name="key_variables">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	396 <param name="type" type="select" label="Keys for accessing variables">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	397 <option value="var_names">All variables in `.var_names`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	398 <option value="obs">All fields in `.obs`</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	399 <option value="custom">Subset of variables in `adata.var_names` or fields of `.obs`"</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	400 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	401 <when value="var_names"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	402 <when value="obs"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	403 <when value="custom">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	404 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from `.var_names` or fields of `.obs`"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	405 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	406 </conditional>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	407 <expand macro="param_groupby"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	408 <expand macro="param_log"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	409 <expand macro="param_use_raw"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	410 <expand macro="section_violin_plots"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	411 <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to `groupby` if `rotation` is `None`, otherwise, no label is shown."/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	412 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	413 <expand macro="seaborn_violinplot"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	414 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	415 <when value="pl.matrixplot">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	416 <expand macro="params_plots"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	417 <expand macro="param_swap_axes"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	418 <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	419 <param argument="cmap" type="select" label="Color palette">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	420 <expand macro="seaborn_color_palette_options"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	421 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	422 <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	423 <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	424 <expand macro="param_matplotlib_pyplot_edgecolors"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	425 <expand macro="param_alpha"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	426 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	427 </section>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	428 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	429 <when value="pl.clustermap">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	430 <param argument="obs_keys" type="text" value="" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported."/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	431 <expand macro="param_use_raw"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	432 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	433 <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	434 <option value="single">single: Nearest Point Algorithm</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	435 <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	436 <option value="average">average: UPGMA algorithm</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	437 <option value="weighted">weighted: WPGMA algorithm</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	438 <option value="centroid">centroid: UPGMC algorithm</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	439 <option value="median">median: WPGMC algorithm</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	440 <option value="ward">ward: incremental algorithm</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	441 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	442 <param name="metric" type="select" label="Distance metric to use for the data" help="See scipy.spatial.distance.pdist documentation for more options https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	443 <expand macro="distance_metric_options"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	444 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	445 <param name="z_score" type="select" label="Calculate z-scores for the rows or the columns?" help="Z scores are: z = (x - mean)/std, so values in each row (column) will get the mean of the row (column) subtracted, then divided by the standard deviation of the row (column). This ensures that each row (column) has mean of 0 and variance of 1.">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	446 <option value="None">No Z-score</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	447 <option value="0">Rows</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	448 <option value="1">Columns</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	449 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	450 <param name="standard_scale" type="select" label="Standardize a dimension?" help="It means for each row or column, subtract the minimum and divide each by its maximum.">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	451 <option value="None">No standardization</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	452 <option value="0">Rows</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	453 <option value="1">Columns</option>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	454 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	455 <param name="col_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the columns?" help=""/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	456 <param name="row_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the rows?" help=""/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	457 </section>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	458 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	459 <when value="pl.highest_expr_genes">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	460 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	461 <param argument="gene_symbols" type="text" optional="true" label="Key for field in `.var` that stores gene symbols" help="Fill it if you do not want to use `.var_names`."/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	462 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	463 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	464 <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	465 <expand macro="seaborn_color_palette_options"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	466 </param>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	467 <param argument="saturation" type="float" value="1" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	468 </section>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	469 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	470 <when value="pl.pca">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	471 <expand macro="param_color"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	472 <expand macro="param_use_raw"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	473 <expand macro="param_sort_order"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	474 <expand macro="pl_groups"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	475 <expand macro="pl_attribute_section"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	476 <expand macro="section_matplotlib_pyplot_scatter"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	477 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	478 <when value="pl.pca_loadings">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	479 <param argument="components" type="text" value="1,2,3" label="Lsit of comma-separated components" help="1, 2, 3 means first, second and third principal components"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	480 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	481 <when value="pl.pca_variance_ratio">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	482 <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	483 <expand macro="param_log"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	484 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	485 <when value="pl.pca_overview">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	486 <expand macro="param_color"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	487 <expand macro="param_use_raw"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	488 <expand macro="param_sort_order"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	489 <expand macro="pl_groups"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	490 <expand macro="pl_attribute_section"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	491 <expand macro="section_matplotlib_pyplot_scatter"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	492 </when>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	493 <when value="pl.tsne">
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	494 <expand macro="param_color"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	495 <expand macro="param_use_raw"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	496 <expand macro="pl_edges"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	497 <expand macro="param_arrows"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	498 <expand macro="param_sort_order"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	499 <expand macro="pl_groups"/>
729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	500 <expand macro="pl_attribute_section"/>

0

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1 <tool id="scanpy_plot" name="Plot with scanpy" version="@galaxy_version@">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

2 <description></description>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

3 <macros>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

4 <import>macros.xml</import>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

5 </macros>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

6 <expand macro="requirements"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

7 <stdio>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

8 <regex match="... storing" source="stderr" level="warning"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

9 </stdio>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

10 <expand macro="version_command"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

11 <command detect_errors="exit_code"><![CDATA[

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

12 @CMD@

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

13 ]]></command>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

14 <configfiles>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

15 <configfile name="script_file"><![CDATA[

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

16 @CMD_imports@

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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17 @CMD_read_inputs@

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18

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

19 sc.settings.figdir = '.'

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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20

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

21 #if $method.method == 'pl.scatter'

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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22

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

23 sc.pl.scatter(

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

24 @CMD_param_plot_inputs@

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

25 #if $method.type.type == 'xy'

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

26 x='$method.type.x',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

27 y='$method.type.y',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

28 layers=('$method.type.layer_x', '$method.type.layer_y', '$method.type.layer_color'),

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

29 #else

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

30 basis='$method.type.basis',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

31 #if str($method.type.color) != ''

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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32 #set $color = ([x.strip() for x in str($method.type.color).split(',')])

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

33 color=$color,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

34 #else

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

35 color=None,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

36 #end if

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

37 #end if

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

38 use_raw=$method.use_raw,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

39 sort_order=$method.sort_order,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

40 @CMD_params_pl_groups@

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

41 @CMD_params_pl_components@

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

42 projection='$method.plot.projection',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

43 legend_loc='$method.plot.legend_loc',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

44 legend_fontsize=$method.plot.legend_fontsize,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

45 legend_fontweight='$method.plot.legend_fontweight',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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46 color_map='$method.plot.color_map',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

47 palette='$method.plot.palette',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

48 frameon=$method.plot.frameon,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

49 #if $method.plot.title

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

50 title='$method.plot.title',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

51 #end if

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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52 size=$method.plot.size)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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53

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

54 #elif $method.method == 'pl.heatmap'

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

55 sc.pl.heatmap(

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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56 @CMD_param_plot_inputs@

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

57 @CMD_params_plots@

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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58 swap_axes=$method.swap_axes,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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59 show_gene_labels=$method.show_gene_labels,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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60 cmap='$method.matplotlib_pyplot_imshow.cmap',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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61 interpolation='$method.matplotlib_pyplot_imshow.interpolation',

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

62 #if $method.matplotlib_pyplot_imshow.alpha

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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63 alpha=$method.matplotlib_pyplot_imshow.alpha,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

64 #end if

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

65 #if $method.matplotlib_pyplot_imshow.vmin

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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66 vmin=$method.matplotlib_pyplot_imshow.vmin,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

67 #end if

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

68 #if $method.matplotlib_pyplot_imshow.vmax

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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69 vmax=$method.matplotlib_pyplot_imshow.vmax,

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

70 #end if

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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71 origin='$method.matplotlib_pyplot_imshow.origin')

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72

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

73 #elif $method.method == 'pl.dotplot'

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parents:

diff changeset

74 sc.pl.dotplot(

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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75 @CMD_param_plot_inputs@

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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diff changeset

76 @CMD_params_plots@

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77 color_map='$method.color_map',

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78 #if $method.dot_max

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79 dot_max=$method.dot_max,

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80 #end if

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81 #if $method.dot_min

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82 dot_min=$method.dot_min,

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83 #end if

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84 @CMD_params_matplotlib_pyplot_scatter@)

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85

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86 #elif $method.method == 'pl.violin'

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87 sc.pl.violin(

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88 @CMD_param_plot_inputs@

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89 #if $method.key_variables.type == "var_names"

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90 #set $key_list = adata.var_names

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91 #elif $method.key_variables.type == "obs"

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92 #set $key_list = adata.obs.select_dtypes(exclude=['category']).columns

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93 #elif $method.key_variables.type == "custom"

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94 #set $key_list=([x.strip() for x in str($method.key_variables.keys).split(',')])

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95 #end if

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96 keys=$key_list,

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97 #if $method.groupby

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98 groupby='$method.groupby',

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99 #end if

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100 log=$method.log,

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101 use_raw=$method.use_raw,

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102 sstripplot=$method.violin_plot.stripplot.stripplot,

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103 #if $method.violin_plot.stripplot.stripplot == "True"

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104 jitter=$method.violin_plot.stripplot.jitter.jitter,

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105 #if $method.violin_plot.stripplot.jitter.jitter == "True"

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106 size=$method.violin_plot.stripplot.jitter.size,

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107 #end if

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108 #end if

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109 multi_panel=$method.violin_plot.multi_panel.multi_panel,

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110 scale='$method.violin_plot.scale',

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111 #if $method.xlabel

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112 xlabel='$method.xlabel',

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113 #end if

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114 #if $method.rotation

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115 rotation=$method.rotation,

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116 #end if

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117 @CMD_params_seaborn_violinplot@)

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118

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119 #elif $method.method == 'pl.matrixplot'

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120 sc.pl.matrixplot(

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121 @CMD_param_plot_inputs@

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122 @CMD_params_plots@

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123 swap_axes=$method.swap_axes,

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124 cmap='$method.matplotlib_pyplot_pcolor.cmap',

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125 #if $method.matplotlib_pyplot_pcolor.vmin

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126 vmin=$method.matplotlib_pyplot_pcolor.vmin,

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127 #end if

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128 #if $method.matplotlib_pyplot_pcolor.vmax

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129 vmax=$method.matplotlib_pyplot_pcolor.vmax,

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130 #end if

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131 edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors',

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132 #if $method.matplotlib_pyplot_pcolor.alpha

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133 alpha=$method.matplotlib_pyplot_pcolor.alpha,

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134 #end if

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135 snap=$method.matplotlib_pyplot_pcolor.snap)

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136

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137 #elif $method.method == 'pl.clustermap'

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138 sc.pl.clustermap(

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139 #if str($method.use_raw) == 'True'

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140 adata=adata.X,

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141 #else

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142 adata=adata,

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143 #end if

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144 show=False,

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145 obs_keys='$method.obs_keys',

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146 use_raw=$method.use_raw,

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147 method='$method.seaborn_clustermap.method',

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148 metric='$method.seaborn_clustermap.metric',

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149 #if str($method.seaborn_clustermap.z_score) == 'None'

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150 z_score=None,

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151 #else

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152 z_score=$method.seaborn_clustermap.z_score,

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153 #end if

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154 #if str($method.seaborn_clustermap.standard_scale) == 'None'

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155 standard_scale=None,

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156 #else

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157 standard_scale=$method.seaborn_clustermap.standard_scale,

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158 #end if

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159 col_cluster=$method.seaborn_clustermap.col_cluster,

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160 row_cluster=$method.seaborn_clustermap.row_cluster).savefig(fname="output.$format")

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161

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162 #elif $method.method == 'pl.highest_expr_genes'

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163 sc.pl.highest_expr_genes(

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164 @CMD_param_plot_inputs@

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165 n_top=$method.n_top,

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166 #if str($method.gene_symbols) != ''

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167 gene_symbols='$method.gene_symbols',

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168 #end if

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169 #if str($method.setseaborn_boxplot.color) != ''

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170 color='$method.setseaborn_boxplot.color',

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171 #end if

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172 #if str($method.setseaborn_boxplot.palette) != 'None'

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173 palette='$method.setseaborn_boxplot.palette',

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174 #end if

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175 saturation=$method.setseaborn_boxplot.saturation)

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176

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177 #elif $method.method == 'pl.pca'

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178 sc.pl.pca(

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179 @CMD_param_plot_inputs@

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180 @CMD_param_color@

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181 use_raw=$method.use_raw,

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182 sort_order=$method.sort_order,

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183 @CMD_params_pl_groups@

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184 @CMD_params_pl_components@

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185 @CMD_pl_attribute_section@

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186 @CMD_params_matplotlib_pyplot_scatter@)

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187

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188 #elif $method.method == 'pl.pca_loadings'

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189 sc.pl.pca_loadings(

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190 @CMD_param_plot_inputs@

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191 #set $components = ([int(x.strip()) for x in str($method.components).split(',')])

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192 components=$components)

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193

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194 #elif $method.method == 'pl.pca_variance_ratio'

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195 sc.pl.pca_variance_ratio(

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196 @CMD_param_plot_inputs@

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197 n_pcs=$method.n_pcs,

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198 log=$method.log)

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199

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200 #elif $method.method == 'pl.pca_overview'

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201 sc.pl.pca_overview(

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202 @CMD_param_plot_inputs@

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203 @CMD_param_color@

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204 use_raw=$method.use_raw,

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205 sort_order=$method.sort_order,

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206 @CMD_params_pl_groups@

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207 @CMD_params_pl_components@

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208 @CMD_pl_attribute_section@

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209 @CMD_params_matplotlib_pyplot_scatter@)

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210

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211 #elif $method.method == 'pl.tsne'

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212 sc.pl.tsne(

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213 @CMD_param_plot_inputs@

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214 @CMD_param_color@

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215 use_raw=$method.use_raw,

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216 @CMD_pl_edges@

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217 arrows=$method.arrows,

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218 sort_order=$method.sort_order,

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219 @CMD_params_pl_groups@

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220 @CMD_params_pl_components@

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221 @CMD_pl_attribute_section@

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222 @CMD_params_matplotlib_pyplot_scatter@)

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223

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224 #elif $method.method == 'pl.umap'

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225 sc.pl.umap(

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226 @CMD_param_plot_inputs@

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227 @CMD_param_color@

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228 use_raw=$method.use_raw,

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229 @CMD_pl_edges@

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230 arrows=$method.arrows,

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231 sort_order=$method.sort_order,

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232 @CMD_params_pl_groups@

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233 @CMD_params_pl_components@

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234 @CMD_pl_attribute_section@

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235 @CMD_params_matplotlib_pyplot_scatter@)

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236

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237 #elif $method.method == 'pl.diffmap'

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238 sc.pl.diffmap(

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239 @CMD_param_plot_inputs@

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240 @CMD_param_color@

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241 use_raw=$method.use_raw,

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242 sort_order=$method.sort_order,

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243 @CMD_params_pl_groups@

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244 @CMD_params_pl_components@

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245 @CMD_pl_attribute_section@

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246 @CMD_params_matplotlib_pyplot_scatter@)

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247

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248 #elif $method.method == 'pl.dpt_groups_pseudotime'

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249 sc.pl.dpt_groups_pseudotime(

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250 @CMD_param_plot_inputs@

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251 color_map='$method.color_map')

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252

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253 #elif $method.method == 'pl.dpt_timeseries'

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254 sc.pl.dpt_timeseries(

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255 @CMD_param_plot_inputs@

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256 #if $method.heatmap.as_heatmap == "True"

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257 color_map='$method.heatmap.color_map',

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258 #end if

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259 as_heatmap=$method.heatmap.as_heatmap)

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260

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261 #elif $method.method == 'pl.paga'

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262 sc.pl.paga(

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263 @CMD_param_plot_inputs@

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264 @CMD_params_pl_paga@)

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265 #end if

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266 ]]></configfile>

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267 </configfiles>

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268 <inputs>

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269 <expand macro="inputs_anndata"/>

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270 <expand macro="param_plot_format"/>

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271 <conditional name="method">

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272 <param argument="method" type="select" label="Method used for plotting">

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273 <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using `pl.scatter`</option>

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274 <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using `pl.heatmap`</option>

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275 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using `pl.dotplot`</option>

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276 <option value="pl.violin">Generic: Violin plot, using `pl.violin`</option>

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277

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278 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using `pl.matrixplot`</option>

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279 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using `pl.clustermap`</option>

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280

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281 <option value="pl.highest_expr_genes">Preprocessing: Plot the fraction of counts assigned to each gene over all cells, using `pl.highest_expr_genes`</option>

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282

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283

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284

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285 <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using `pl.pca`</option>

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286 <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using `pl.pca_loadings`</option>

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287 <option value="pl.pca_variance_ratio">PCA: Scatter plot in PCA coordinates, using `pl.pca_variance_ratio`</option>

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288 <option value="pl.pca_overview">PCA: Plot PCA results, using `pl.pca_overview`</option>

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289 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using `pl.tsne`</option>

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290 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using `pl.umap`</option>

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291 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using `pl.diffmap`</option>

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292

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293 <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using `pl.dpt_groups_pseudotime`</option>

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294 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using `pl.dpt_timeseries`</option>

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295 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using `pl.paga`</option>

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296

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297

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298

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299

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300

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301

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302

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303

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304

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305

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306

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307

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308

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309

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310 </param>

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311 <when value="pl.scatter">

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312 <conditional name="type">

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313 <param name="type" type="select" label="Plotting tool that computed coordinates" help="">

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314 <option value="xy">Using coordinates</option>

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315 <option value="basis">Using tool that computes coordinates</option>

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316 </param>

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317 <when value="xy">

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318 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either `.obs` or `.var`"/>

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319 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either `.obs` or `.var`"/>

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320 <param argument="layer_x" type="text" value="X" label="Layers for x coordinate" help="Use the `layers` attribute of `adata` if present"/>

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321 <param argument="layer_y" type="text" value="X" label="Layers for y coordinate" help="Use the `layers` attribute of `adata` if present"/>

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322 <param argument="layer_color" type="text" value="X" label="Layers for color" help="Use the `layers` attribute of `adata` if present"/>

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323 </when>

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324 <when value="basis">

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325 <param argument="basis" type="select" label="Plotting tool that computes coordinates" help="">

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326 <option value="pca">pca (need to run on `tl.pca` output)</option>

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327 <option value="tsne">tsne (need to run on `tl.tsne` output)</option>

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328 <option value="umap">umap (need to run on `tl.umap` output)</option>

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329 <option value="diffmap">diffmap (need to run on `tl.diffmap` output)</option>

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330 <option value="draw_graph_fr">draw_graph_fr (need to run on `tl.draw_graph` output)</option>

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331 </param>

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332 <expand macro="param_color"/>

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333 </when>

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334 </conditional>

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335 <expand macro="param_use_raw"/>

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336 <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot data points with higher values on top of others?" help="For continuous annotations used as color parameter"/>

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337 <expand macro="pl_groups"/>

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338 <section name="plot" title="Plot attributes">

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339 <expand macro="pl_components"/>

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340 <expand macro="param_projection"/>

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341 <expand macro="param_legend_loc"/>

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342 <expand macro="param_legend_fontsize"/>

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343 <expand macro="param_legend_fontweight"/>

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344 <expand macro="param_color_map"/>

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345 <expand macro="param_palette"/>

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346 <expand macro="param_frameon"/>

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347 <expand macro="param_size"/>

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348 <expand macro="param_title"/>

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349 </section>

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350 </when>

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351 <when value="pl.heatmap">

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352 <expand macro="params_plots"/>

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353 <expand macro="param_swap_axes"/>

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354 <param argument="show_gene_labels" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show gene labels?" help="By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed."/>

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355 <section name="matplotlib_pyplot_imshow" title="Parameters for matplotlib.pyplot.imshow">

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356 <expand macro="param_cmap"/>

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357 <param name="interpolation" type="select" label="Interpolation method" help="">

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358 <option value="none">none</option>

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359 <option value="nearest">nearest</option>

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360 <option value="bilinear">bilinear</option>

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361 <option value="bicubic">bicubic</option>

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362 <option value="spline16">spline16</option>

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363 <option value="spline36">spline36</option>

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364 <option value="hanning">hanning</option>

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365 <option value="hamming">hamming</option>

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366 <option value="hermite">hermite</option>

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367 <option value="kaiser">kaiser</option>

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368 <option value="quadric">quadric</option>

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369 <option value="catrom">catrom</option>

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370 <option value="gaussian">gaussian</option>

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371 <option value="bessel">bessel</option>

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372 <option value="sinc">sinc</option>

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373 <option value="mitchell">mitchell</option>

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374 <option value="lanczos">lanczos</option>

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375 </param>

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376 <expand macro="param_alpha"/>

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377 <expand macro="param_vmin"/>

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378 <expand macro="param_vmax"/>

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379 <param name="origin" type="select" label="Place the [0,0] index of the array in the upper left or lower left corner of the axes" help=" The convention 'upper' is typically used for matrices and images.">

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380 <option value="upper">Upper</option>

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381 <option value="lower">Lower</option>

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382 </param>

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383 </section>

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384 </when>

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385 <when value="pl.dotplot">

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386 <expand macro="params_plots"/>

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387 <param argument="color_map" type="select" label="Color palette">

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388 <expand macro="matplotlib_pyplot_colormap"/>

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389 </param>

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390 <param argument="dot_max" type="float" value="" min="0" max="1" optional="true" label="Maximum dot size" help="If none, the maximum dot size is set to the maximum fraction value found (e.g. 0.6). If given, the value should be a number between 0 and 1. All fractions larger than dot_max are clipped to this value."/>

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391 <param argument="dot_min" type="float" value="" min="0" max="1" optional="true" label="Minimum dot size" help="If none, the minimum dot size is set to 0. If given, the value should be a number between 0 and 1. All fractions smaller than dot_min are clipped to this value."/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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392 <expand macro="section_matplotlib_pyplot_scatter"/>

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393 </when>

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394 <when value="pl.violin">

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395 <conditional name="key_variables">

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396 <param name="type" type="select" label="Keys for accessing variables">

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397 <option value="var_names">All variables in `.var_names`</option>

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398 <option value="obs">All fields in `.obs`</option>

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399 <option value="custom">Subset of variables in `adata.var_names` or fields of `.obs`"</option>

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400 </param>

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401 <when value="var_names"/>

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402 <when value="obs"/>

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403 <when value="custom">

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404 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from `.var_names` or fields of `.obs`"/>

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405 </when>

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406 </conditional>

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407 <expand macro="param_groupby"/>

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408 <expand macro="param_log"/>

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409 <expand macro="param_use_raw"/>

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410 <expand macro="section_violin_plots"/>

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411 <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to `groupby` if `rotation` is `None`, otherwise, no label is shown."/>

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412 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>

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413 <expand macro="seaborn_violinplot"/>

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414 </when>

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415 <when value="pl.matrixplot">

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416 <expand macro="params_plots"/>

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417 <expand macro="param_swap_axes"/>

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418 <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">

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419 <param argument="cmap" type="select" label="Color palette">

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420 <expand macro="seaborn_color_palette_options"/>

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421 </param>

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422 <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>

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423 <param argument="vmax" type="float" value="" optional="true" label="Maximum value to anchor the colormap" help=""/>

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424 <expand macro="param_matplotlib_pyplot_edgecolors"/>

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425 <expand macro="param_alpha"/>

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426 <param argument="snap" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Snap the mesh to pixel boundaries?" help=""/>

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427 </section>

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428 </when>

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429 <when value="pl.clustermap">

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430 <param argument="obs_keys" type="text" value="" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported."/>

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431 <expand macro="param_use_raw"/>

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432 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">

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433 <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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434 <option value="single">single: Nearest Point Algorithm</option>

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435 <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option>

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436 <option value="average">average: UPGMA algorithm</option>

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437 <option value="weighted">weighted: WPGMA algorithm</option>

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438 <option value="centroid">centroid: UPGMC algorithm</option>

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439 <option value="median">median: WPGMC algorithm</option>

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440 <option value="ward">ward: incremental algorithm</option>

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441 </param>

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442 <param name="metric" type="select" label="Distance metric to use for the data" help="See scipy.spatial.distance.pdist documentation for more options https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html">

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diff changeset

443 <expand macro="distance_metric_options"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

444 </param>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

445 <param name="z_score" type="select" label="Calculate z-scores for the rows or the columns?" help="Z scores are: z = (x - mean)/std, so values in each row (column) will get the mean of the row (column) subtracted, then divided by the standard deviation of the row (column). This ensures that each row (column) has mean of 0 and variance of 1.">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

446 <option value="None">No Z-score</option>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

447 <option value="0">Rows</option>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

448 <option value="1">Columns</option>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

449 </param>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

450 <param name="standard_scale" type="select" label="Standardize a dimension?" help="It means for each row or column, subtract the minimum and divide each by its maximum.">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

451 <option value="None">No standardization</option>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

452 <option value="0">Rows</option>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

453 <option value="1">Columns</option>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

454 </param>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

455 <param name="col_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the columns?" help=""/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

456 <param name="row_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the rows?" help=""/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

457 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

458 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

459 <when value="pl.highest_expr_genes">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

460 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

461 <param argument="gene_symbols" type="text" optional="true" label="Key for field in `.var` that stores gene symbols" help="Fill it if you do not want to use `.var_names`."/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

462 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

463 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help=""/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

464 <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

465 <expand macro="seaborn_color_palette_options"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

466 </param>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

467 <param argument="saturation" type="float" value="1" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

468 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

469 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

470 <when value="pl.pca">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

471 <expand macro="param_color"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

472 <expand macro="param_use_raw"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

473 <expand macro="param_sort_order"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

474 <expand macro="pl_groups"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

475 <expand macro="pl_attribute_section"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

476 <expand macro="section_matplotlib_pyplot_scatter"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

477 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

478 <when value="pl.pca_loadings">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

479 <param argument="components" type="text" value="1,2,3" label="Lsit of comma-separated components" help="1, 2, 3 means first, second and third principal components"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

480 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

481 <when value="pl.pca_variance_ratio">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

482 <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

483 <expand macro="param_log"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

484 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

485 <when value="pl.pca_overview">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

486 <expand macro="param_color"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

487 <expand macro="param_use_raw"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

488 <expand macro="param_sort_order"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

489 <expand macro="pl_groups"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

490 <expand macro="pl_attribute_section"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

491 <expand macro="section_matplotlib_pyplot_scatter"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

492 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

493 <when value="pl.tsne">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

494 <expand macro="param_color"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

495 <expand macro="param_use_raw"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

496 <expand macro="pl_edges"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

497 <expand macro="param_arrows"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

498 <expand macro="param_sort_order"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

499 <expand macro="pl_groups"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

500 <expand macro="pl_attribute_section"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

501 <expand macro="section_matplotlib_pyplot_scatter"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

502 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

503 <when value="pl.umap">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

504 <expand macro="param_color"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

505 <expand macro="param_use_raw"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

506 <expand macro="pl_edges"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

507 <expand macro="param_arrows"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

508 <expand macro="param_sort_order"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

509 <expand macro="pl_groups"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

510 <expand macro="pl_attribute_section"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

511 <expand macro="section_matplotlib_pyplot_scatter"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

512 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

513 <when value="pl.diffmap">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

514 <expand macro="param_color"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

515 <expand macro="param_use_raw"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

516 <expand macro="param_sort_order"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

517 <expand macro="pl_groups"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

518 <expand macro="pl_attribute_section"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

519 <expand macro="section_matplotlib_pyplot_scatter"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

520 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

521 <when value="pl.dpt_groups_pseudotime">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

522 <expand macro="param_color_map"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

523 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

524 <when value="pl.dpt_timeseries">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

525 <conditional name="heatmap">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

526 <param argument="as_heatmap" type="select" label="Plot the timeseries as heatmap?" help="">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

527 <option value="True">Yes</option>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

528 <option value="False">No</option>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

529 </param>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

530 <when value="True">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

531 <expand macro="param_color_map"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

532 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

533 <when value="False" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

534 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

535 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

536 <when value="pl.paga">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

537 <expand macro="inputs_paga"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

538 </when>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

539 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

540 </inputs>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

541 <outputs>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

542 <data name="out_png" format="png" from_work_dir="*.png" label="${tool.name} on ${on_string}">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

543 <filter>format == 'png'</filter>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

544 </data>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

545 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="${tool.name} on ${on_string}">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

546 <filter>format == 'pdf'</filter>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

547 </data>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

548 <data name="out_svg" format="svg" from_work_dir="*.svg" label="${tool.name} on ${on_string}">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

549 <filter>format == 'svg'</filter>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

550 </data>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

551 </outputs>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

552 <tests>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

553 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

554

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

555 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

556 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

557 <param name="adata" value="pp.pca.krumsiek11.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

558 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

559 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

560 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

561 <param name="method" value="pl.scatter"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

562 <conditional name="type">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

563 <param name="type" value="basis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

564 <param name="basis" value="pca"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

565 <param name="color" value="EgrNab, Gata2"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

566 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

567 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

568 <param name="sort_order" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

569 <section name="plot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

570 <param name="projection" value="2d"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

571 <param name="legend_loc" value="right margin"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

572 <param name="legend_fontsize" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

573 <param name="legend_fontweight" value="normal"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

574 <param name="color_map" value="inferno"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

575 <param name="palette" value="inferno"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

576 <param name="frameon" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

577 <param name="size" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

578 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

579 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

580 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

581 <has_text_matching expression="sc.pl.scatter"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

582 <has_text_matching expression="basis='pca'" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

583 <has_text_matching expression="color=\['EgrNab', 'Gata2'\]"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

584 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

585 <has_text_matching expression="sort_order=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

586 <has_text_matching expression="groups=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

587 <has_text_matching expression="components=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

588 <has_text_matching expression="projection='2d'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

589 <has_text_matching expression="legend_loc='right margin'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

590 <has_text_matching expression="legend_fontsize=1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

591 <has_text_matching expression="legend_fontweight='normal'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

592 <has_text_matching expression="color_map='inferno'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

593 <has_text_matching expression="palette='inferno'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

594 <has_text_matching expression="frameon=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

595 <has_text_matching expression="size=1.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

596 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

597 <output name="out_png" file="pl.scatter.pca.krumsiek11.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

598 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

599 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

600

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

601 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

602 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

603 <param name="adata" value="krumsiek11.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

604 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

605 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

606 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

607 <param name="method" value="pl.scatter"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

608 <conditional name="type">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

609 <param name="type" value="xy"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

610 <param name="x" value="EKLF"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

611 <param name="y" value="Cebpa"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

612 <param name="layer_x" value="X"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

613 <param name="layer_y" value="X"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

614 <param name="layer_color" value="X"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

615 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

616 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

617 <param name="sort_order" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

618 <section name="plot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

619 <param name="projection" value="2d"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

620 <param name="legend_loc" value="right margin"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

621 <param name="legend_fontsize" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

622 <param name="legend_fontweight" value="normal"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

623 <param name="palette" value="bwr"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

624 <param name="frameon" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

625 <param name="size" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

626 <param name="title" value="A title"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

627 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

628 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

629 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

630 <has_text_matching expression="sc.pl.scatter"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

631 <has_text_matching expression="x='EKLF'" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

632 <has_text_matching expression="y='Cebpa'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

633 <has_text_matching expression="layers=$'X', 'X', 'X'$"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

634 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

635 <has_text_matching expression="sort_order=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

636 <has_text_matching expression="groups=None,"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

637 <has_text_matching expression="components=None,"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

638 <has_text_matching expression="projection='2d'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

639 <has_text_matching expression="legend_loc='right margin'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

640 <has_text_matching expression="legend_fontsize=1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

641 <has_text_matching expression="legend_fontweight='normal'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

642 <has_text_matching expression="color_map='viridis'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

643 <has_text_matching expression="palette='bwr'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

644 <has_text_matching expression="frameon=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

645 <has_text_matching expression="size=1.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

646 <has_text_matching expression="title='A title'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

647 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

648 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

649 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

650 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

651

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

652 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

653 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

654 <param name="adata" value="krumsiek11.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

655 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

656 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

657 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

658 <param name="method" value="pl.heatmap"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

659 <conditional name="var_names">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

660 <param name="type" value="all"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

661 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

662 <param name="groupby" value="cell_type"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

663 <param name="log" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

664 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

665 <param name="num_categories" value="7"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

666 <conditional name="figsize">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

667 <param name="test" value="yes"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

668 <param name="width" value="10" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

669 <param name="height" value="3"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

670 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

671 <param name="dendrogram" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

672 <param name="swap_axes" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

673 <param name="show_gene_labels" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

674 <section name="matplotlib_pyplot_imshow">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

675 <param name="cmap" value="YlGnBu"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

676 <param name="interpolation" value="none"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

677 <param name="origin" value="upper"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

678 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

679 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

680 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

681 <has_text_matching expression="sc.pl.heatmap"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

682 <has_text_matching expression="var_names=adata.var_names" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

683 <has_text_matching expression="groupby='cell_type'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

684 <has_text_matching expression="log=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

685 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

686 <has_text_matching expression="num_categories=7"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

687 <has_text_matching expression="dendrogram=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

688 <has_text_matching expression="var_group_positions=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

689 <has_text_matching expression="var_group_labels=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

690 <has_text_matching expression="figsize=$10, 3$"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

691 <has_text_matching expression="swap_axes=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

692 <has_text_matching expression="show_gene_labels=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

693 <has_text_matching expression="interpolation='none'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

694 <has_text_matching expression="cmap='YlGnBu'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

695 <has_text_matching expression="origin='upper'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

696 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

697 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

698 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

699 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

700

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

701 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

702 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

703 <param name="adata" value="pbmc68k_reduced.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

704 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

705 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

706 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

707 <param name="method" value="pl.dotplot"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

708 <conditional name="var_names">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

709 <param name="type" value="custom"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

710 <param name="var_names" value="CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

711 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

712 <param name="groupby" value="louvain"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

713 <param name="log" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

714 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

715 <param name="num_categories" value="7"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

716 <param name="dendrogram" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

717 <conditional name="figsize">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

718 <param name="test" value="no"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

719 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

720 <param name="dendrogram" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

721 <repeat name="var_group_positions">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

722 <param name="start" value="0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

723 <param name="end" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

724 <param name="label" value="B cells"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

725 </repeat>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

726 <repeat name="var_group_positions">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

727 <param name="start" value="11"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

728 <param name="end" value="12"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

729 <param name="label" value="dendritic"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

730 </repeat>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

731 <param name="color_map" value="hot"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

732 <param name="dot_max" value="0.7"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

733 <param name="dot_min" value="0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

734 <section name="matplotlib_pyplot_scatter">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

735 <param name="linewidths" value="0" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

736 <param name="edgecolors" value="face"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

737 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

738 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

739 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

740 <has_text_matching expression="sc.pl.dotplot"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

741 <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

742 <has_text_matching expression="groupby='louvain'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

743 <has_text_matching expression="log=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

744 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

745 <has_text_matching expression="num_categories=7"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

746 <has_text_matching expression="dendrogram=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

747 <has_text_matching expression="var_group_positions=\[$0, 1$, $11, 12$\]"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

748 <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

749 <has_text_matching expression="color_map='hot'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

750 <has_text_matching expression="dot_max=0.7"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

751 <has_text_matching expression="dot_min=0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

752 <has_text_matching expression="linewidths=0.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

753 <has_text_matching expression="edgecolors='face'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

754 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

755 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

756 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

757 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

758

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

759 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

760 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

761 <param name="adata" value="pbmc68k_reduced.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

762 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

763 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

764 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

765 <param name="method" value="pl.violin"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

766 <conditional name="key_variables">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

767 <param name="type" value="custom"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

768 <param name="keys" value="n_genes, percent_mito, n_counts" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

769 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

770 <param name="log" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

771 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

772 <section name="violin_plot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

773 <conditional name="stripplot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

774 <param name="stripplot" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

775 <param name="jitter" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

776 <param name="size" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

777 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

778 <conditional name="multi_panel">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

779 <param name="multi_panel" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

780 <param name="width" value="20"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

781 <param name="height" value="20"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

782 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

783 <param name="scale" value="width"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

784 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

785 <section name="seaborn_violinplot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

786 <param name="bw" value="scott"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

787 <param name="linewidth" value="0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

788 <param name="color" value="AliceBlue"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

789 <param name="palette" value="viridis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

790 <param name="saturation" value="0.75"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

791 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

792 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

793 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

794 <has_text_matching expression="sc.pl.violin"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

795 <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

796 <has_text_matching expression="log=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

797 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

798 <has_text_matching expression="sstripplot=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

799 <has_text_matching expression="jitter=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

800 <has_text_matching expression="size=1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

801 <has_text_matching expression="multi_panel=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

802 <has_text_matching expression="scale='width'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

803 <has_text_matching expression="bw='scott'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

804 <has_text_matching expression="scale='width'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

805 <has_text_matching expression="linewidth=0.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

806 <has_text_matching expression="color='AliceBlue'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

807 <has_text_matching expression="palette='viridis'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

808 <has_text_matching expression="saturation=0.75"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

809 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

810 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

811 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

812 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

813

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

814 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

815 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

816 <param name="adata" value="krumsiek11.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

817 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

818 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

819 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

820 <param name="method" value="pl.matrixplot"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

821 <conditional name="var_names">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

822 <param name="type" value="all"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

823 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

824 <param name="groupby" value="cell_type"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

825 <param name="log" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

826 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

827 <param name="num_categories" value="7"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

828 <param name="dendrogram" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

829 <conditional name="figsize">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

830 <param name="test" value="no"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

831 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

832 <param name="swap_axes" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

833 <section name="matplotlib_pyplot_pcolor">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

834 <param name="cmap" value="viridis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

835 <param name="edgecolors" value="face"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

836 <param name="snap" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

837 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

838 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

839 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

840 <has_text_matching expression="sc.pl.matrixplot"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

841 <has_text_matching expression="var_names=adata.var_names" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

842 <has_text_matching expression="groupby='cell_type'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

843 <has_text_matching expression="log=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

844 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

845 <has_text_matching expression="num_categories=7"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

846 <has_text_matching expression="dendrogram=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

847 <has_text_matching expression="var_group_positions=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

848 <has_text_matching expression="var_group_labels=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

849 <has_text_matching expression="swap_axes=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

850 <has_text_matching expression="cmap='viridis'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

851 <has_text_matching expression="edgecolors='face'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

852 <has_text_matching expression="snap=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

853 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

854 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

855 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

856 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

857

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

858 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

859 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

860 <param name="adata" value="krumsiek11.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

861 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

862 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

863 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

864 <param name="method" value="pl.clustermap"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

865 <param name="obs_keys" value="cell_type"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

866 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

867 <section name="seaborn_clustermap">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

868 <param name="method" value="single"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

869 <param name="metric" value="braycurtis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

870 <param name="z_score" value="None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

871 <param name="standard_scale" value="None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

872 <param name="col_cluster" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

873 <param name="row_cluster" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

874 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

875 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

876 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

877 <has_text_matching expression="sc.pl.clustermap"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

878 <has_text_matching expression="adata=adata" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

879 <has_text_matching expression="obs_keys='cell_type'" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

880 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

881 <has_text_matching expression="method='single'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

882 <has_text_matching expression="metric='braycurtis'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

883 <has_text_matching expression="z_score=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

884 <has_text_matching expression="standard_scale=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

885 <has_text_matching expression="col_cluster=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

886 <has_text_matching expression="row_cluster=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

887 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

888 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

889 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

890 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

891

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

892 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

893 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

894 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

895 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

896 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

897 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

898 <param name="method" value="pl.highest_expr_genes"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

899 <param name="n_top" value="30"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

900 <param name="gene_symbols" value="means"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

901 <section name="setseaborn_boxplot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

902 <param name="color" value="blue"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

903 <param name="saturation" value="0.5"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

904 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

905 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

906 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

907 <has_text_matching expression="sc.pl.highest_expr_genes"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

908 <has_text_matching expression="n_top=30" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

909 <has_text_matching expression="gene_symbols='means'" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

910 <has_text_matching expression="color='blue'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

911 <has_text_matching expression="saturation=0.5"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

912 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

913 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

914 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

915 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

916

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

917 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

918 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

919 <param name="adata" value="pbmc68k_reduced.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

920 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

921 <param name="format" value="pdf"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

922 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

923 <param name="method" value="pl.pca"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

924 <param name="color" value="CD3D,CD79A"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

925 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

926 <param name="sort_order" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

927 <section name="plot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

928 <repeat name="components">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

929 <param name="axis1" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

930 <param name="axis2" value="2"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

931 </repeat>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

932 <repeat name="components">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

933 <param name="axis1" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

934 <param name="axis2" value="3"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

935 </repeat>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

936 <param name="projection" value="2d"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

937 <param name="legend_loc" value="right margin"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

938 <param name="legend_fontsize" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

939 <param name="legend_fontweight" value="normal"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

940 <param name="size" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

941 <param name="palette" value="viridis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

942 <param name="frameon" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

943 <param name="ncols" value="2"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

944 <param name="wspace" value="0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

945 <param name="hspace" value="0.25"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

946 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

947 <section name="matplotlib_pyplot_scatter">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

948 <param name="linewidths" value="0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

949 <param name="edgecolors" value="face"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

950 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

951 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

952 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

953 <has_text_matching expression="sc.pl.pca"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

954 <has_text_matching expression="save='.pdf'" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

955 <has_text_matching expression="color=\['CD3D', 'CD79A'\]" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

956 <has_text_matching expression="use_raw=False" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

957 <has_text_matching expression="sort_order=True" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

958 <has_text_matching expression="groups=None" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

959 <has_text_matching expression="components=\['1,2', '1,3'\]" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

960 <has_text_matching expression="projection='2d'" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

961 <has_text_matching expression="legend_loc='right margin'" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

962 <has_text_matching expression="legend_fontsize=1" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

963 <has_text_matching expression="legend_fontweight='normal'" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

964 <has_text_matching expression="size=1.0" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

965 <has_text_matching expression="palette='viridis'" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

966 <has_text_matching expression="frameon=True" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

967 <has_text_matching expression="ncols=2" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

968 <has_text_matching expression="wspace=0.1" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

969 <has_text_matching expression="hspace=0.25" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

970 <has_text_matching expression="linewidths=0.0" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

971 <has_text_matching expression="edgecolors='face" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

972 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

973 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

974 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

975 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

976

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

977 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

978 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

979 <param name="adata" value="pp.pca.krumsiek11.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

980 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

981 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

982 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

983 <param name="method" value="pl.pca_loadings"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

984 <param name="components" value="1,2,3"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

985 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

986 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

987 <has_text_matching expression="sc.pl.pca_loadings"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

988 <has_text_matching expression="components=\[1, 2, 3\]" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

989 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

990 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

991 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

992 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

993

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

994 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

995 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

996 <param name="adata" value="pp.pca.krumsiek11.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

997 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

998 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

999 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1000 <param name="method" value="pl.pca_variance_ratio"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1001 <param name="n_pcs" value="5"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1002 <param name="log" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1003 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1004 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1005 <has_text_matching expression="sc.pl.pca_variance_ratio"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1006 <has_text_matching expression="n_pcs=5" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1007 <has_text_matching expression="log=False" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1008 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1009 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1010 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1011 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1012

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1013 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1014 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1015 <param name="adata" value="pp.pca.krumsiek11.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1016 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1017 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1018 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1019 <param name="method" value="pl.pca_overview"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1020 <param name="color" value="cell_type"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1021 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1022 <param name="sort_order" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1023 <section name="plot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1024 <param name="projection" value="3d"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1025 <param name="legend_loc" value="right margin"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1026 <param name="legend_fontsize" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1027 <param name="legend_fontweight" value="normal"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1028 <param name="size" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1029 <param name="palette" value="viridis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1030 <param name="frameon" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1031 <param name="ncols" value="4"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1032 <param name="wspace" value="0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1033 <param name="hspace" value="0.25"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1034 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1035 <section name="matplotlib_pyplot_scatter">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1036 <param name="linewidths" value="0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1037 <param name="edgecolors" value="face"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1038 <param name="vmin" value="-5"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1039 <param name="vmax" value="5"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1040 <param name="edgecolors" value="face"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1041 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1042 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1043 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1044 <has_text_matching expression="sc.pl.pca_overview"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1045 <has_text_matching expression="color=\['cell_type'\]"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1046 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1047 <has_text_matching expression="sort_order=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1048 <has_text_matching expression="groups=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1049 <has_text_matching expression="components=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1050 <has_text_matching expression="projection='3d'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1051 <has_text_matching expression="legend_loc='right margin'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1052 <has_text_matching expression="legend_fontsize=1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1053 <has_text_matching expression="legend_fontweight='normal'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1054 <has_text_matching expression="size=1.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1055 <has_text_matching expression="palette='viridis'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1056 <has_text_matching expression="frameon=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1057 <has_text_matching expression="ncols=4"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1058 <has_text_matching expression="wspace=0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1059 <has_text_matching expression="hspace=0.25"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1060 <has_text_matching expression="vmin=-5.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1061 <has_text_matching expression="vmax=5.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1062 <has_text_matching expression="linewidths=0.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1063 <has_text_matching expression="edgecolors='face'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1064 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1065 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1066 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1067 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1068

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1069 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1070 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1071 <param name="adata" value="tl.tsne.krumsiek11.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1072 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1073 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1074 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1075 <param name="method" value="pl.tsne"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1076 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1077 <conditional name="edges">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1078 <param name="edges" value="False" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1079 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1080 <param name="arrows" value="False" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1081 <param name="sort_order" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1082 <section name="plot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1083 <param name="projection" value="2d"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1084 <param name="legend_loc" value="right margin"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1085 <param name="legend_fontsize" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1086 <param name="legend_fontweight" value="normal"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1087 <param name="palette" value="viridis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1088 <param name="frameon" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1089 <param name="size" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1090 <param name="ncols" value="4"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1091 <param name="wspace" value="0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1092 <param name="hspace" value="0.25"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1093 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1094 <section name="matplotlib_pyplot_scatter">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1095 <param name="linewidths" value="0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1096 <param name="edgecolors" value="face"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1097 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1098 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1099 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1100 <has_text_matching expression="sc.pl.tsne"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1101 <has_text_matching expression="color=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1102 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1103 <has_text_matching expression="edges=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1104 <has_text_matching expression="arrows=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1105 <has_text_matching expression="sort_order=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1106 <has_text_matching expression="groups=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1107 <has_text_matching expression="components=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1108 <has_text_matching expression="projection='2d'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1109 <has_text_matching expression="legend_loc='right margin'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1110 <has_text_matching expression="legend_fontsize=1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1111 <has_text_matching expression="legend_fontweight='normal'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1112 <has_text_matching expression="size=1.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1113 <has_text_matching expression="palette='viridis'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1114 <has_text_matching expression="frameon=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1115 <has_text_matching expression="ncols=4"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1116 <has_text_matching expression="wspace=0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1117 <has_text_matching expression="hspace=0.25"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1118 <has_text_matching expression="linewidths=0.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1119 <has_text_matching expression="edgecolors='face'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1120 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1121 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1122 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1123 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1124

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1125 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1126 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1127 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1128 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1129 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1130 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1131 <param name="method" value="pl.umap"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1132 <param name="color" value="paul15_clusters"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1133 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1134 <conditional name="edges">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1135 <param name="edges" value="True" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1136 <param name="edges_width" value="0.1" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1137 <param name="edges_color" value="AliceBlue"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1138 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1139 <param name="arrows" value="False" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1140 <section name="plot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1141 <param name="projection" value="2d"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1142 <param name="legend_loc" value="right margin"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1143 <param name="legend_fontsize" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1144 <param name="legend_fontweight" value="normal"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1145 <param name="size" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1146 <param name="palette" value="viridis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1147 <param name="frameon" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1148 <param name="ncols" value="4"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1149 <param name="wspace" value="0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1150 <param name="hspace" value="0.25"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1151 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1152 <section name="matplotlib_pyplot_scatter">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1153 <param name="linewidths" value="0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1154 <param name="edgecolors" value="face"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1155 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1156 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1157 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1158 <has_text_matching expression="sc.pl.umap"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1159 <has_text_matching expression="color=\['paul15_clusters'\]"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1160 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1161 <has_text_matching expression="edges=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1162 <has_text_matching expression="edges_width=0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1163 <has_text_matching expression="edges_color='AliceBlue'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1164 <has_text_matching expression="arrows=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1165 <has_text_matching expression="sort_order=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1166 <has_text_matching expression="groups=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1167 <has_text_matching expression="components=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1168 <has_text_matching expression="projection='2d'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1169 <has_text_matching expression="legend_loc='right margin'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1170 <has_text_matching expression="legend_fontsize=1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1171 <has_text_matching expression="legend_fontweight='normal'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1172 <has_text_matching expression="size=1.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1173 <has_text_matching expression="palette='viridis'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1174 <has_text_matching expression="frameon=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1175 <has_text_matching expression="ncols=4"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1176 <has_text_matching expression="wspace=0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1177 <has_text_matching expression="hspace=0.25"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1178 <has_text_matching expression="linewidths=0.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1179 <has_text_matching expression="edgecolors='face'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1180 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1181 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1182 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1183 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1184

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1185 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1186 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1187 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1188 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1189 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1190 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1191 <param name="method" value="pl.diffmap"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1192 <param name="color" value="paul15_clusters"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1193 <param name="use_raw" value="False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1194 <param name="sort_order" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1195 <section name="plot">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1196 <param name="projection" value="2d"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1197 <param name="legend_loc" value="right margin"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1198 <param name="legend_fontsize" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1199 <param name="legend_fontweight" value="normal"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1200 <param name="size" value="1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1201 <param name="palette" value="viridis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1202 <param name="frameon" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1203 <param name="ncols" value="4"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1204 <param name="wspace" value="0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1205 <param name="hspace" value="0.25"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1206 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1207 <section name="matplotlib_pyplot_scatter">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1208 <param name="linewidths" value="0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1209 <param name="edgecolors" value="face"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1210 </section>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1211 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1212 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1213 <has_text_matching expression="sc.pl.diffmap"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1214 <has_text_matching expression="color=\['paul15_clusters'\]"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1215 <has_text_matching expression="use_raw=False"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1216 <has_text_matching expression="sort_order=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1217 <has_text_matching expression="groups=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1218 <has_text_matching expression="components=None"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1219 <has_text_matching expression="projection='2d'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1220 <has_text_matching expression="legend_loc='right margin'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1221 <has_text_matching expression="legend_fontsize=1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1222 <has_text_matching expression="legend_fontweight='normal'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1223 <has_text_matching expression="size=1.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1224 <has_text_matching expression="palette='viridis'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1225 <has_text_matching expression="frameon=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1226 <has_text_matching expression="ncols=4"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1227 <has_text_matching expression="wspace=0.1"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1228 <has_text_matching expression="hspace=0.25"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1229 <has_text_matching expression="linewidths=0.0"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1230 <has_text_matching expression="edgecolors='face'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1231 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1232 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1233 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1234 <!--<test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1235 < test pl.dpt_groups_pseudotime >

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1236 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1237 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1238 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1239 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1240 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1241 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1242 <param name="method" value="pl.dpt_groups_pseudotime"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1243 <param name="color_map" value="viridis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1244 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1245 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1246 <has_text_matching expression="sc.pl.dpt_groups_pseudotime"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1247 <has_text_matching expression="color_map='viridis'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1248 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1249 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1250 </test>!-->

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1251 <test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1252

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1253 <conditional name="input">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1254 <param name="format" value="h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1255 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad" />

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1256 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1257 <param name="format" value="png"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1258 <conditional name="method">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1259 <param name="method" value="pl.dpt_timeseries"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1260 <conditional name="heatmap">

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1261 <param name="as_heatmap" value="True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1262 <param name="color_map" value="viridis"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1263 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1264 </conditional>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1265 <assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1266 <has_text_matching expression="sc.pl.dpt_timeseries"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1267 <has_text_matching expression="color_map='viridis'"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1268 <has_text_matching expression="as_heatmap=True"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1269 </assert_stdout>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1270 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1271 </test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1272 <!--<test>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1273 test pl.paga

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1274 <conditional name="input">

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1275 <param name="format" value="h5ad" />

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1276 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />

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1277 </conditional>

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1278 <param name="format" value="png"/>

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1279 <conditional name="method">

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1280 <param name="method" value="pl.paga"/>

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1281 <param name="threshold" value="0.01"/>

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1282 <param name="color" value="paul15_clusters"/>

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1283 <param name="labels" value="label" />

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1284 <param name="layout" value="fr"/>

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1285 <param name="random_state" value="0"/>

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1286 <param name="solid_edges" value="connectivities"/>

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1287 <param name="single_component" value="False"/>

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1288 <param name="fontsize" value="1"/>

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1289 <param name="node_size_scale" value="1.0"/>

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1290 <param name="node_size_power" value="0.5"/>

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1291 <param name="edge_width_scale" value="5"/>

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1292 <param name="arrowsize" value="30"/>

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1293 <param name="normalize_to_color" value="False"/>

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1294 <param name="cmap" value="viridis"/>

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1295 <param name="frameon" value="True"/>

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1296 </conditional>

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1297 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="sim_size"/>

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1298 </test>!-->

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1299 </tests>

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1300 <help><![CDATA[

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1301 Generic: Scatter plot along observations or variables axes (`pl.scatter`)

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1302 =========================================================================

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1303

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1304 Color the plot using annotations of observations (`.obs`), variables

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1305 (`.var`) or expression of genes (`.var_names`).

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1306

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1307 More details on the `scanpy documentation

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1308 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.scatter.html>`__

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1309

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1310 Generic: Heatmap of the expression values of set of genes (`pl.heatmap`)

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1311 ========================================================================

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1312

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1313 If `groupby` is given, the heatmap is ordered by the respective group. For

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1314 example, a list of marker genes can be plotted, ordered by clustering. If

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1315 the `groupby` observation annotation is not categorical the observation

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1316 annotation is turned into a categorical by binning the data into the number

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1317 specified in `num_categories`.

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1318

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1319 More details on the `scanpy documentation

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1320 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.heatmap.html>`__

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1321

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1322 Generic: Makes a dot plot of the expression values (`pl.dotplot`)

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1323 =================================================================

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1324

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1325 For each var_name and each `groupby` category a dot is plotted. Each dot

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1326 represents two values: mean expression within each category (visualized by

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1327 color) and fraction of cells expressing the var_name in the

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1328 category. (visualized by the size of the dot). If groupby is not given, the

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1329 dotplot assumes that all data belongs to a single category. A gene is not

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1330 considered expressed if the expression value in the adata (or adata.raw) is

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1331 equal to zero.

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1332

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1333 For instance, for each marker gene, the mean value and the percentage of cells

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1334 expressing the gene can be visualized for each cluster.

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1335

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1336 More details on the `scanpy documentation

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1337 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.dotplot.html>`__

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1338

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1339 Generic: Violin plot (`pl.violin`)

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1340 ==================================

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1341

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1342 Wraps `seaborn.violinplot` for `anndata.AnnData`.

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1343

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1344 More details on the `scanpy documentation

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1345 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.stacked_violin.html>`__

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1346

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1347 Generic: Heatmap of the mean expression values per cluster (`pl.matrixplot`)

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1348 ============================================================================

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1349

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1350 Creates a heatmap of the mean expression values per cluster of each var_names

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1351

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1352 If groupby is not given, the matrixplot assumes that all data belongs to a single

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1353 category.

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1354

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1355 More details on the `scanpy documentation

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1356 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.matrixplot.html>`__

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1357

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1358 Generic: Hierarchically-clustered heatmap (`pl.clustermap`)

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1359 ===========================================================

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1360

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1361 Wraps `seaborn.clustermap

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1362 <https://seaborn.pydata.org/generated/seaborn.clustermap.html>`__ for

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1363 `anndata.AnnData`.

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1364

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1365 The returned object has a savefig() method that should be used if you want

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diff changeset

1366 to save the figure object without clipping the dendrograms.

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1367

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1368 To access the reordered row indices, use:

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1369 clustergrid.dendrogram_row.reordered_ind

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1370

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1371 Column indices, use: clustergrid.dendrogram_col.reordered_ind

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1372

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1373 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1374 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.clustermap.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1375

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1376 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1377 =========================================================================================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1378

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1379 Computes, for each gene, the fraction of counts assigned to that gene within

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1380 a cell. The `n_top` genes with the highest mean fraction over all cells are

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1381 plotted as boxplots.

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1382

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1383 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`, see `here

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

1384 <https://bioconductor.org/packages/devel/bioc/vignettes/scater/inst/doc/vignette-qc.html>`__.

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1385 -- Davis McCarthy and Aaron Lun

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1386

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1387 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1388 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.highest_expr_genes.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1389

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1390 PCA: Scatter plot in PCA coordinates (`pl.pca`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1391 ===============================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1392

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1393 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1394 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.pca.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1395

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1396 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1397 =====================================================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1398

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1399 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1400 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.pca_loadings.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1401

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1402 PCA: Plot the variance ratio (`pl.pca_variance_ratio`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1403 ======================================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1404

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1405 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1406 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.pca_variance_ratio.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1407

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1408 PCA: Plot PCA results (`pl.pca_overview`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1409 =========================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1410

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1411 The parameters are the ones of the scatter plot. Call pca_ranking separately

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1412 if you want to change the default settings.

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1413

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1414 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1415 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.pca_overview.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1416

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1417 Embedding: Scatter plot in tSNE basis (`pl.tsne`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1418 =================================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1419

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1420 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1421 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.tsne.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1422

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1423 Embeddings: Scatter plot in UMAP basis (`pl.umap`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1424 ==================================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1425

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1426 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1427 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.umap.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1428

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1429 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1430 ==============================================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1431

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1432 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1433 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.diffmap.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1434

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1435 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1436 ===========================================================================================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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parents:

diff changeset

1437

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1438 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1439 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.dpt_groups_pseudotime.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1440

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1441 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1442 =====================================================================================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1443

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1444 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1445 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.dpt_timeseries.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1446

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1447

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1448 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1449 ====================================================================================================================================

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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parents:

diff changeset

1450

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1451 This uses ForceAtlas2 or igraph's layout algorithms for most layouts.

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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parents:

diff changeset

1452

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1453 When initializing the positions, note that - for some reason - igraph

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1454 mirrors coordinates along the x axis... that is, you should increase the

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1455 `maxiter` parameter by 1 if the layout is flipped.

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1456

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

diff changeset

1457 More details on the `scanpy documentation

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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diff changeset

1458 <https://scanpy.readthedocs.io/en/latest/api/scanpy.pl.paga.html>`__

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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1459

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

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1460

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

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1461 ]]></help>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

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1462 <expand macro="citations"/>

729198e3330c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6

iuc

parents:

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1463 </tool>

Mercurial > repos > iuc > scanpy_plot

annotate plot.xml @ 0:729198e3330c draft