diff macros.xml @ 12:1f380e8a6aec draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c21958f44b81d740191999fb6015d5ae69538ee0

--- a/macros.xml	Wed Sep 22 21:07:11 2021 +0000
+++ b/macros.xml	Wed Jul 31 18:07:15 2024 +0000
@@ -1,12 +1,17 @@
 <macros>
-    <token name="@version@">1.7.1</token>
-    <token name="@profile@">19.01</token>
-    <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
+    <token name="@TOOL_VERSION@">1.9.6</token>
+    <token name="@VERSION_SUFFIX@">4</token>
+    <token name="@profile@">21.09</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@version@">scanpy</requirement>
-            <requirement type="package" version="2.0.17">loompy</requirement>
-            <requirement type="package" version="0.8.3">leidenalg</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
+            <requirement type="package" version="3.0.6">loompy</requirement>
+            <requirement type="package" version="0.10.1">leidenalg</requirement>
+            <requirement type="package" version="0.8.1">louvain</requirement>
+            <requirement type="package" version="1.5.3">pandas</requirement>
+            <requirement type="package" version="3.7">matplotlib</requirement>
+            <requirement type="package" version="0.12.2">seaborn</requirement>
+            <requirement type="package" version="3.0.0">magic-impute</requirement>
             <yield />
         </requirements>
     </xml>
@@ -15,9 +20,15 @@
             <xref type="bio.tools">scanpy</xref>
         </xrefs>
     </xml>
+    <xml name="creators">
+        <creator>
+            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
+        </creator>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1186/s13059-017-1382-0</citation>
+            <citation type="doi">10.1093/gigascience/giaa102</citation>
         </citations>
     </xml>
     <xml name="version_command">
@@ -56,7 +67,7 @@
         <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
     </xml>
     <token name="@CMD_read_inputs@"><![CDATA[
-adata = sc.read('anndata.h5ad')
+adata = sc.read_h5ad('anndata.h5ad')
 ]]>
     </token>
     <xml name="inputs_common_advanced">
@@ -66,12 +77,12 @@
     </xml>
     <xml name="anndata_outputs">
         <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
-        <data name="hidden_output" format="txt" label="Log file" >
+            <data name="hidden_output" format="txt" label="Log file" >
             <filter>advanced_common['show_log']</filter>
         </data>
     </xml>
     <token name="@CMD_anndata_write_outputs@"><![CDATA[
-adata.write('anndata.h5ad')
+adata.write_h5ad('anndata.h5ad')
 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
     print(adata, file=ainfo)
 ]]>
@@ -414,6 +425,7 @@
             <param name="type" type="select" label="Variables to plot (columns of the heatmaps)" >
                 <option value="all">All variables in 'adata.var_names'</option>
                 <option value="custom">Subset of variables in 'adata.var_names'</option>
+                <option value="customfile">Subset of variables as a tabular file</option>
             </param>
             <when value="all"/>
             <when value="custom">
@@ -421,6 +433,9 @@
                     <expand macro="sanitize_query" />
                 </param>
             </when>
+            <when value="customfile">
+                <param argument="var_names" type="data" format="tabular" label="List of variables to plot" help="This should be a tsv where row = group (e.g. celltypes) and columns = variables."></param>
+            </when>
         </conditional>
     </xml>
     <xml name="param_num_categories">
@@ -457,15 +472,17 @@
         <expand macro="param_num_categories"/>
     </xml>
     <token name="@CMD_params_inputs@"><![CDATA[
-    #if $method.var_names.type == 'all'
-    var_names=adata.var_names,
-#else
+    #if $method.var_names.type == 'custom'
     #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
     var_names=$var_names,
-#end if
-#if str($method.groupby) != ''
+    #else if $method.var_names.type == 'customfile'
+    var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0).to_dict(orient='index').items()},
+    #else
+    var_names=adata.var_names,
+    #end if
+    #if $method.groupby
     groupby='$method.groupby',
-#end if
+    #end if
     num_categories=$method.num_categories,
     ]]></token>
     <xml name="params_plots">
@@ -491,15 +508,15 @@
     var_group_positions=$var_group_positions,
     var_group_labels=$var_group_labels,
     #end if
-#if $method.var_group_rotation
-    var_group_rotation=$method.var_group_rotation,
-#end if
-#if $method.figsize.test == 'yes'
-    figsize=($method.figsize.width, $method.figsize.height),
-#end if
-#if $method.layer != ''
-    layer='$method.layer',
-#end if
+    #if str($method.var_group_rotation) != ''
+        var_group_rotation=$method.var_group_rotation,
+    #end if
+    #if $method.figsize.test == 'yes'
+        figsize=($method.figsize.width, $method.figsize.height),
+    #end if
+    #if $method.layer
+        layer='$method.layer',
+    #end if
     ]]></token>
     <xml name="matplotlib_color">
         <option value="AliceBlue">AliceBlue</option>
@@ -652,9 +669,8 @@
         <option value="YellowGreen">YellowGreen</option>
     </xml>
     <xml name="param_matplotlib_pyplot_edgecolors">
-        <param argument="edgecolors" type="select" label="Edge color of the marker" help="">
+        <param argument="edgecolors" type="select" optional="true" label="Edge color of the marker" help="">
             <option value="face">The edge color will always be the same as the face color</option>
-            <option value="none">No patch boundary will be drawn</option>
             <expand macro="matplotlib_color"/>
         </param>
     </xml>
@@ -692,17 +708,19 @@
         </section>
     </xml>
     <token name="@CMD_params_matplotlib_pyplot_scatter@"><![CDATA[
-    #if $method.matplotlib_pyplot_scatter.vmin
+    #if str($method.matplotlib_pyplot_scatter.vmin) != ''
     vmin=$method.matplotlib_pyplot_scatter.vmin,
     #end if
-    #if $method.matplotlib_pyplot_scatter.vmax
+    #if str($method.matplotlib_pyplot_scatter.vmax) != ''
     vmax=$method.matplotlib_pyplot_scatter.vmax,
     #end if
-    #if $method.matplotlib_pyplot_scatter.alpha
+    #if str($method.matplotlib_pyplot_scatter.alpha) != ''
     alpha=$method.matplotlib_pyplot_scatter.alpha,
     #end if
-    linewidths=$method.matplotlib_pyplot_scatter.linewidths,
-    edgecolors='$method.matplotlib_pyplot_scatter.edgecolors'
+    lw=$method.matplotlib_pyplot_scatter.linewidths,
+    #if $method.matplotlib_pyplot_scatter.edgecolors
+    ec='$method.matplotlib_pyplot_scatter.edgecolors'
+    #end if
     ]]></token>
     <xml name="conditional_stripplot">
         <conditional name="stripplot">
@@ -742,13 +760,7 @@
         </param>
     </xml>
     <token name="@CMD_params_violin_plots@"><![CDATA[
-    stripplot=$method.violin_plot.stripplot.stripplot,
-#if $method.violin_plot.stripplot.stripplot == "True"
-    jitter=$method.violin_plot.stripplot.jitter.jitter,
-    #if $method.violin_plot.stripplot.jitter.jitter == "True"
-    size=$method.violin_plot.stripplot.jitter.size,
-    #end if
-#end if
+    @CMD_conditional_stripplot@
     multi_panel=$method.violin_plot.multi_panel.multi_panel,
 #if $method.multi_panel.violin_plot.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
     figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height)
@@ -766,7 +778,7 @@
                 <option value="h">horizontal</option>
             </param>
             <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/>
-            <param argument="color" type="select" label="Color for all of the elements" help="">
+            <param argument="color" type="select" optional="true" label="Color for all of the elements" help="">
                 <expand macro="matplotlib_color"/>
             </param>
             <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
@@ -778,7 +790,9 @@
     orient='$method.seaborn_violinplot.orient',
 #end if
     linewidth=$method.seaborn_violinplot.linewidth,
+    #if $method.seaborn_violinplot.color
     color='$method.seaborn_violinplot.color',
+    #end if
     saturation=$method.seaborn_violinplot.saturation
     ]]></token>
     <xml name="param_color">
@@ -787,7 +801,7 @@
         </param>
     </xml>
     <token name="@CMD_param_color@"><![CDATA[
-#if str($method.color) != ''
+#if $method.color
     #set $color = ([x.strip() for x in str($method.color).split(',')])
     color=$color,
 #end if
@@ -798,7 +812,7 @@
         </param>
     </xml>
     <token name="@CMD_params_groups@"><![CDATA[
-#if str($method.groups) != ''
+#if $method.groups
     #set $groups=([x.strip() for x in str($method.groups).split(',')])
     groups=$groups,
 #end if
@@ -868,14 +882,12 @@
         </param>
     </xml>
     <xml name="param_palette">
-        <param argument="palette" type="select" label="Colors to use for plotting categorical annotation groups" help="">
-            <option value="default">Default</option>
+        <param argument="palette" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
     <xml name="param_color_map">
-        <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
-            <option value="None">Default</option>
+        <param argument="color_map" type="select" optional="true" label="Color map to use for continous variables" help="">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
@@ -931,7 +943,7 @@
             </param>
             <when value="True">
                 <param argument="edges_width" type="float" min="0" value="0.1" label="Width of edges"/>
-                <param argument="edges_color" type="select" label="Color of edges">
+                <param argument="edges_color" type="select" optional="true" label="Color of edges">
                     <expand macro="matplotlib_color"/>
                 </param>
             </when>
@@ -942,7 +954,9 @@
 #if str($method.edges.edges) == 'True'
     edges=True,
     edges_width=$method.edges.edges_width,
+    #if $method.edges.edges_color
     edges_color='$method.edges.edges_color',
+    #end if
 #else
     edges=False,
 #end if
@@ -952,7 +966,7 @@
         <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
     </xml>
     <xml name="param_cmap">
-        <param argument="cmap" type="select" label="Colors to use for plotting categorical annotation groups" help="">
+        <param argument="cmap" type="select" optional="true" label="Colors to use for plotting categorical annotation groups" help="">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
     </xml>
@@ -979,10 +993,10 @@
     @CMD_param_legend_fontsize@
     legend_fontweight='$method.plot.legend_fontweight',
     @CMD_param_size@
-    #if str($method.plot.color_map) != 'None'
+    #if $method.plot.color_map
     color_map='$method.plot.color_map',
     #end if
-    #if str($method.plot.palette) != ''
+    #if $method.plot.palette
     palette='$method.plot.palette',
     #end if
     frameon=$method.plot.frameon,
@@ -1052,18 +1066,18 @@
     </xml>
     <token name="@CMD_params_pl_paga@"><![CDATA[
     threshold=$method.threshold,
-#if str($method.groups) != ''
+#if $method.groups
     #set $groups=([x.strip() for x in str($method.groups).split(',')])
     groups=$groups,
 #end if
-#if str($method.color) != ''
+#if $method.color
     #set $color=([x.strip() for x in str($method.color).split(',')])
     color=$color,
 #end if
 #if $method.pos
     pos=np.fromfile($method.pos, dtype=dt),
 #end if
-#if str($method.labels) != ''
+#if $method.labels
     #set $labels=([x.strip() for x in str($method.labels).split(',')])
     labels=$labels,
 #end if
@@ -1072,7 +1086,7 @@
     init_pos=np.fromfile($method.init_pos, dtype=dt),
 #end if
     random_state=$method.random_state,
-#if str($method.root) != ''
+#if $method.root
     #set $root=([int(x.strip()) for x in str($method.root).split(',')])
     root=$root,
 #end if
@@ -1088,15 +1102,17 @@
     node_size_scale=$method.node_size_scale,
     node_size_power=$method.node_size_power,
     edge_width_scale=$method.edge_width_scale,
-#if $method.min_edge_width
+#if str($method.min_edge_width) != ''
     min_edge_width=$method.min_edge_width,
 #end if
-#if $method.max_edge_width
+#if str($method.max_edge_width) != ''
     max_edge_width=$method.max_edge_width,
 #end if
     arrowsize=$method.arrowsize,
     normalize_to_color=$method.normalize_to_color,
+    #if $method.cmap
     cmap='$method.cmap',
+    #end if
 #if $method.title
     title='$method.title',
 #end if
@@ -1112,10 +1128,10 @@
         </param>
     </xml>
     <xml name="param_n_genes">
-        <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help=""/>
+        <param argument="n_genes" type="integer" min="0" value="10" label="Number of genes to show" help="It is only used if you are not specifying certain variable names"/>
     </xml>
     <xml name="pl_dotplot">
-        <param argument="color_map" type="select" label="Color palette">
+        <param argument="color_map" type="select" optional="true" label="Color palette">
             <expand macro="matplotlib_pyplot_colormap"/>
         </param>
         <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."/>
@@ -1123,7 +1139,9 @@
         <expand macro="section_matplotlib_pyplot_scatter"/>
     </xml>
     <token name="@CMD_pl_dotplot@"><![CDATA[
+    #if $method.color_map
     color_map='$method.color_map',
+    #end if
     #if str($method.dot_max) != ''
     dot_max=$method.dot_max,
     #end if
@@ -1174,17 +1192,19 @@
     <token name="@CMD_pl_heatmap@"><![CDATA[
     swap_axes=$method.swap_axes,
     show_gene_labels=$method.show_gene_labels,
+    #if $method.matplotlib_pyplot_imshow.cmap
     cmap='$method.matplotlib_pyplot_imshow.cmap',
+    #end if
     #if str($method.matplotlib_pyplot_imshow.interpolation) != 'None'
     interpolation='$method.matplotlib_pyplot_imshow.interpolation',
     #end if
-    #if $method.matplotlib_pyplot_imshow.alpha
+    #if str($method.matplotlib_pyplot_imshow.alpha) != ''
     alpha=$method.matplotlib_pyplot_imshow.alpha,
     #end if
-    #if $method.matplotlib_pyplot_imshow.vmin
+    #if str($method.matplotlib_pyplot_imshow.vmin) != ''
     vmin=$method.matplotlib_pyplot_imshow.vmin,
     #end if
-    #if $method.matplotlib_pyplot_imshow.vmax
+    #if str($method.matplotlib_pyplot_imshow.vmax) != ''
     vmax=$method.matplotlib_pyplot_imshow.vmax,
     #end if
     origin='$method.matplotlib_pyplot_imshow.origin'
@@ -1197,10 +1217,8 @@
     </xml>
     <token name="@CMD_pl_rank_genes_groups_ext@"><![CDATA[
     @CMD_params_groups@
-    #if str($method.n_genes) != ''
     n_genes=$method.n_genes,
-    #end if
-    #if str($method.key) != ''
+    #if $method.key
     key='$method.key',
     #end if
     ]]>
@@ -1208,7 +1226,7 @@
     <xml name="pl_matrixplot">
         <expand macro="param_swap_axes"/>
         <section name="matplotlib_pyplot_pcolor" title="Parameters for matplotlib.pyplot.pcolor">
-            <param argument="cmap" type="select" label="Color palette">
+            <param argument="cmap" type="select" optional="true" label="Color palette">
                 <expand macro="seaborn_color_palette_options"/>
             </param>
             <param argument="vmin" type="float" value="" optional="true" label="Minimum value to anchor the colormap" help=""/>
@@ -1220,15 +1238,19 @@
     </xml>
     <token name="@CMD_pl_matrixplot@"><![CDATA[
     swap_axes=$method.swap_axes,
+    #if $method.matplotlib_pyplot_pcolor.cmap
     cmap='$method.matplotlib_pyplot_pcolor.cmap',
-    #if $method.matplotlib_pyplot_pcolor.vmin
+    #end if
+    #if str($method.matplotlib_pyplot_pcolor.vmin) != ''
     vmin=$method.matplotlib_pyplot_pcolor.vmin,
     #end if
-    #if $method.matplotlib_pyplot_pcolor.vmax
+    #if str($method.matplotlib_pyplot_pcolor.vmax) != ''
     vmax=$method.matplotlib_pyplot_pcolor.vmax,
     #end if
-    edgecolors='$method.matplotlib_pyplot_pcolor.edgecolors',
-    #if $method.matplotlib_pyplot_pcolor.alpha
+    #if $method.matplotlib_pyplot_pcolor.edgecolors
+    ec='$method.matplotlib_pyplot_pcolor.edgecolors',
+    #end if
+    #if str($method.matplotlib_pyplot_pcolor.alpha) != ''
     alpha=$method.matplotlib_pyplot_pcolor.alpha,
     #end if
     snap=$method.matplotlib_pyplot_pcolor.snap
@@ -1240,7 +1262,7 @@
             <expand macro="conditional_stripplot"/>
             <expand macro="param_scale"/>
         </section>
-        <param argument="row_palette" type="select" label="Colors to use in each of the stacked violin plots">
+        <param argument="row_palette" type="select" optional="true" label="Colors to use in each of the stacked violin plots">
             <option value="muted">muted</option>
             <expand macro="seaborn_color_palette_options"/>
         </param>
@@ -1255,7 +1277,9 @@
     swap_axes=$method.swap_axes,
     @CMD_conditional_stripplot@
     scale='$method.violin_plot.scale',
+    #if $method.row_palette
     row_palette='$method.row_palette',
+    #end if
     #if str($method.standard_scale) != 'None'
     standard_scale='$method.standard_scale',
     #end if