mimodd_core: cloudmap.xml annotate

annotate cloudmap.xml @ 2:36b4be01cce4 draft default tip

planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty

author	wolma
date	Sat, 11 Nov 2017 16:39:44 -0500
parents	85576338fbcf
children

rev	line source
0 85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	1 <tool id="mimodd_map" name="MiModD NacreousMap" version="@MIMODD_WRAPPER_VERSION@">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	2 <description>maps phenotypically selected variants by multi-variant linkage analysis</description>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	3 <macros>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	4 <import>macros.xml</import>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	5 <macro name="svd_unconditional">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	6 <expand macro="hidden_algo_params" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	7 <expand macro="seqdict_param" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	8 <expand macro="bins" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	9 <conditional name="plotopts">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	10 <param name="plots" type="select" label="graphical output settings">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	11 <option value="-p">Give me graphics.</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	12 <option value="">Do not generate graphs.</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	13 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	14 <when value="">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	15 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	16 <when value="-p">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	17 <expand macro="scatter_default" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	18 <param name="show_kde" type="boolean" truevalue="" falsevalue="--no-kde" checked="true"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	19 label="show kde line in histogram plots"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	20 help="The tool can calculate a kernel density estimate for the linkage data based on a bin size of 10 kilobases and display it as a solid line in the histogram plots." />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	21 <param name="hylim" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	22 label="upper limit for the histogram y-axis (leave blank for automatic scaling)" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	23 <param name="xlim" type="select" label="x-axis scaling">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	24 <option value="">preserve relative contig sizes</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	25 <option value="--fit-width">scale each contig to fit the plot width</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	26 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	27 <expand macro="hist_colors" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	28 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	29 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	30 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	31 <macro name="vaf_unconditional">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	32 <expand macro="bins" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	33 <conditional name="plotopts">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	34 <param name="plots" type="select" label="graphical output settings">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	35 <option value="-p">Give me everything (scatter plots and histograms)</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	36 <option value="--no-scatter -p">Generate only histograms</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	37 <option value="--no-hist -p">Generate only scatter plots</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	38 <option value="">Do not generate graphs.</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	39 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	40 <when value="">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	41 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	42 <when value="--no-scatter -p">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	43 <expand macro="scatter_default" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	44 <param name="show_kde" type="boolean" truevalue="" falsevalue="--no-kde" checked="true"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	45 label="show kde line in histogram plots"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	46 help="The tool can calculate a kernel density estimate for the linkage data based on a bin size of 10 kilobases and display it as a solid line in the histogram plots." />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	47 <param name="hylim" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	48 label="upper limit for the histogram y-axis (leave blank for automatic scaling)" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	49 <param name="xlim" type="select" label="x-axis scaling">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	50 <option value="">preserve relative contig sizes</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	51 <option value="--fit-width">scale each contig to fit the plot width</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	52 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	53 <expand macro="hist_colors" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	54 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	55 <when value="--no-hist -p">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	56 <expand macro="hist_default" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	57 <param name="sylim" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	58 label="upper limit for the scatter plot y-axis (default: 1)" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	59 <param name="xlim" type="select" label="x-axis scaling">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	60 <option value="">preserve relative contig sizes</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	61 <option value="--fit-width">scale each contig to fit the plot width</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	62 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	63 <param name="span" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	64 label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1, specify 0 to prevent calculation)"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	65 help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	66 <expand macro="scatter_colors" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	67 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	68 <when value="-p">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	69 <expand macro="plot_all" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	70 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	71 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	72 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	73 <macro name="vac_unconditional">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	74 <expand macro="bins" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	75 <conditional name="plotopts">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	76 <param name="plots" type="select" label="graphical output settings">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	77 <option value="--no-scatter -p">Give me graphical output</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	78 <option value="">Do not generate graphs.</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	79 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	80 <when value="">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	81 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	82 <when value="--no-scatter -p">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	83 <expand macro="scatter_default" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	84 <param name="show_kde" type="boolean" truevalue="" falsevalue="--no-kde" checked="true"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	85 label="show kde line in histogram plots"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	86 help="The tool can calculate a kernel density estimate for the linkage data based on a bin size of 10 kilobases and display it as a solid line in the histogram plots." />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	87 <param name="hylim" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	88 label="upper limit for the histogram y-axis (leave blank for automatic scaling)" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	89 <param name="xlim" type="select" label="x-axis scaling">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	90 <option value="">preserve relative contig sizes</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	91 <option value="--fit-width">scale each contig to fit the plot width</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	92 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	93 <expand macro="hist_colors" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	94 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	95 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	96 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	97 <macro name="hidden_algo_params">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	98 <param name="sample" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	99 <expand macro="hidden_vaf_algo_params" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	100 <param name="contrast_sample" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	101 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	102 <macro name="hidden_vaf_algo_params">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	103 <param name="related_parent_sample" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	104 <param name="unrelated_parent_sample" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	105 <param name="infer_missing" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	106 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	107 <macro name="bins">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	108 <repeat name="bin_sizes" default="0" min="0" title="bin sizes to analyze variants in (defaults to: 1Mb and 500Kb)"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	109 help="Values can be entered in bases (e.g., 1000000), kilobases (e.g., 500Kb) or megabases (e.g., 1Mb), but must be integral, i.e. no decimal numbers are allowed.">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	110 <param name="bin_size" type="text" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	111 </repeat>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	112 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	113 <macro name="scatter_default">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	114 <param name="sylim" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	115 <param name="span" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	116 <param name="pcols" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	117 <param name="lcols" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	118 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	119 <macro name="hist_default">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	120 <param name="show_kde" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	121 <param name="hylim" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	122 <param name="hcols" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	123 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	124 <macro name="hist_colors">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	125 <repeat name="hcols" default="0" min="0" title="histogram colors"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	126 help="For each bin size chosen above a histogram will be generated with its color selected from the list provided here (defaults to alternating darkgrey, red).">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	127 <param name="hcolor" type="color" value="darkgrey">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	128 <sanitizer><valid><add value="#" /></valid></sanitizer>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	129 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	130 </repeat>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	131 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	132 <macro name="scatter_colors">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	133 <repeat name="pcols" default="0" min="0" title="data point colors"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	134 help="Series of data points will be plotted based on the colors selected here.">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	135 <param name="pcol" type="color" value="black">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	136 <sanitizer><valid><add value="#" /></valid></sanitizer>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	137 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	138 </repeat>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	139 <repeat name="lcols" default="0" min="0"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	140 title="regression line colors"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	141 help="Regression lines through series of data will be plotted in the colors selected here.">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	142 <param name="lcol" type="color" value="red">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	143 <sanitizer><valid><add value="#" /></valid></sanitizer>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	144 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	145 </repeat>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	146 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	147 <macro name="plot_all">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	148 <param name="show_kde" type="boolean" truevalue="" falsevalue="--no-kde" checked="true"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	149 label="show kde line in histogram plots"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	150 help="The tool can calculate a kernel density estimate for the linkage data based on a bin size of 10 kilobases and display it as a solid line in the histogram plots." />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	151 <param name="hylim" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	152 label="upper limit for the histogram y-axis (leave blank for automatic scaling)" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	153 <param name="sylim" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	154 label="upper limit for the scatter plot y-axis (default: 1)" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	155 <param name="xlim" type="select" label="x-axis scaling">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	156 <option value="">preserve relative contig sizes</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	157 <option value="--fit-width">scale each contig to fit the plot width</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	158 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	159 <param name="span" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	160 label="span value to be used in calculating the Loess regression line through the scatter data (default=0.1, specify 0 to prevent calculation)"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	161 help="smaller values give a more responsive curve that often picks up local evidence for tight linkage better, but too small values lead to plotting failures (in that case just rerun the tool with a larger value)." />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	162 <expand macro="hist_colors" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	163 <expand macro="scatter_colors" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	164 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	165 <macro name="seqdict_param">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	166 <conditional name="seqinfo_external">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	167 <param name="source" type="select"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	168 label="does this input provide contig name and size information?"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	169 help="ALWAYS select 'yes' here if the input dataset was generated with MiModD. Input generated with third-party tools may or may not provide the information. If in doubt, execute the job with 'yes' selected and see if you are getting a corresponding error message.">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	170 <option value="">Yes</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	171 <option value="fasta">No, get the information from a reference genome in my history</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	172 <option value="cached">No, get the information from a built-in genome</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	173 <option value="seqdict">No, get the information from a CloudMap-style sequence dictionary in my history</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	174 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	175 <when value="fasta">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	176 <param name="seqinfo" type="data" format="fasta"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	177 label="Reference genome to extract contig info from" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	178 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	179 <when value="cached">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	180 <param name="seqinfo" type="select"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	181 label="Reference genome to extract contig info from">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	182 <options from_data_table="all_fasta" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	183 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	184 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	185 <when value="seqdict">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	186 <param name="seqinfo" type="data" format="tabular"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	187 label="CloudMap-style sequence dictionary to extract contig info from" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	188 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	189 <when value="">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	190 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	191 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	192 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	193 <macro name="test_tabular_out">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	194 <output name="ofile" ftype="tabular">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	195 <assert_contents>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	196 <has_text text="chrI" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	197 <has_text text="chrII" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	198 <has_text text="chrIII" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	199 <has_text text="chrIV" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	200 <has_text text="chrV" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	201 <has_text text="chrX" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	202 <has_text text="MtDNA" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	203 </assert_contents>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	204 </output>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	205 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	206 </macros>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	207 <expand macro="requirements" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	208 <expand macro="stdio" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	209 <expand macro="version_command" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	210 <command><![CDATA[
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	211 mimodd map ${opt.mode} "${opt.source.ifile}"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	212 #if $str($opt.source.sample):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	213 -m '${opt.source.sample}'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	214 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	215 #if $str($opt.source.related_parent_sample):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	216 -r '${opt.source.related_parent_sample}'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	217 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	218 #if $str($opt.source.unrelated_parent_sample):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	219 -u '${opt.source.unrelated_parent_sample}'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	220 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	221 #if $str($opt.source.contrast_sample):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	222 -c '${opt.source.contrast_sample}'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	223 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	224 $opt.source.infer_missing
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	225 -o '$ofile'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	226 #if $str($opt.source.seqinfo_external.source) in ("fasta", "seqdict"):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	227 -s '${opt.source.seqinfo_external.seqinfo}'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	228 #else if $str($opt.source.seqinfo_external.source) == "cached":
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	229 -s '${opt.source.seqinfo_external.seqinfo.fields.path}'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	230 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	231 #if $len($opt.source.bin_sizes):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	232 --bin-sizes
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	233 #for $size in $opt.source.bin_sizes:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	234 '${size.bin_size}'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	235 #end for
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	236 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	237 #if $str($opt.source.tabfile):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	238 $str($opt.source.tabfile) '$tfile'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	239 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	240 #if $str($opt.source.plotopts.plots):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	241 $str($opt.source.plotopts.plots) '$pfile'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	242 $opt.source.plotopts.show_kde
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	243 $str($opt.source.plotopts.xlim)
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	244 #if $str($opt.source.plotopts.hylim):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	245 --ylim-hist $str($opt.source.plotopts.hylim)
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	246 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	247 #if $str($opt.source.plotopts.hcols) and $len($opt.source.plotopts.hcols):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	248 --hist-colors
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	249 #for $color in $opt.source.plotopts.hcols:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	250 '${color.hcolor}'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	251 #end for
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	252 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	253 #if $str($opt.source.plotopts.sylim):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	254 --ylim-scatter $str($opt.source.plotopts.sylim)
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	255 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	256 #if $str($opt.source.plotopts.pcols) and $len($opt.source.plotopts.pcols):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	257 --points-colors
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	258 #for $color in $opt.source.plotopts.pcols:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	259 '${color.pcol}'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	260 #end for
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	261 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	262 #if $str($opt.source.plotopts.lcols) and $len($opt.source.plotopts.lcols):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	263 --loess-colors
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	264 #for $color in $opt.source.plotopts.lcols:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	265 '${color.lcol}'
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	266 #end for
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	267 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	268 #if $str($opt.source.plotopts.span):
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	269 --loess-span $str($opt.source.plotopts.span)
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	270 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	271 #end if
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	272 ]]></command>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	273
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	274 <inputs>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	275 <conditional name="opt">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	276 <param name="mode" type="select" label="type of mapping analysis to perform"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	277 help="Select Simple Variant Density (SVD) Mapping to map mutations based on linked inheritance in near isogenic populations, Variant Allele Frequency (VAF) Mapping for bulk segregant analysis. Select Reprocess for rapidly replotting the result of a previous VAF analysis.">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	278 <option value="SVD">Simple Variant Density Mapping</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	279 <option value="VAF">Variant Allele Frequency Mapping</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	280 <option value="VAC">Variant Allele Contrast Mapping</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	281 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	282 <when value="SVD">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	283 <conditional name="source">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	284 <param name="inputtype" type="select" label="data source to use">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	285 <option value="vcf">VCF file of variants (for de-novo mapping)</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	286 <option value="rep">per-variant report file (for remapping a previous analysis)</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	287 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	288 <when value="vcf">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	289 <param name="ifile" type="data" format="vcf"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	290 label="input file with variants to analyze" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	291 <expand macro="svd_unconditional" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	292 <param name="tabfile" type="select"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	293 label="additional per-variant output file"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	294 help="You can either choose to produce a tabular per-variant report, which is useful for fast replotting with different plot settings, or a VCF-like CloudMap-compatibility output that can be used as input for the older CloudMap EMS Variant Density Mapping tool as an alternative plotting tool.">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	295 <option value="">Do not generate per-variant output</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	296 <option value="-t">Tabular per-variant report</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	297 <option value="--cloudmap -t">CloudMap compatibility output</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	298 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	299 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	300 <when value="rep">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	301 <param name="ifile" type="data" format="tabular,csv"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	302 label="input file with variants to analyze" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	303 <param name="tabfile" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	304 <expand macro="svd_unconditional" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	305 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	306 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	307 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	308 <when value="VAF">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	309 <conditional name="source">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	310 <param name="inputtype" type="select" label="data source to use">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	311 <option value="vcf">VCF file of variants (for de-novo mapping)</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	312 <option value="rep">per-variant report file (for remapping a previous analysis)</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	313 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	314 <when value="vcf">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	315 <param name="ifile" type="data" format="vcf"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	316 label="input file with variants to analyze" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	317 <expand macro="seqdict_param" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	318 <param name="sample" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	319 label="mapping sample name" help="the sample to perform mutation mapping for">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	320 <validator type="empty_field" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	321 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	322 <param name="related_parent_sample" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	323 label="name of the related parent sample"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	324 help="the sample that provides variants present in your original mutant strain or in an ancestor (like the pre-mutagenesis strain); leave blank if not available" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	325 <param name="unrelated_parent_sample" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	326 label="name of the unrelated parent sample"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	327 help="the sample that provides variants present in the unrelated mapping strain (or in an ancestor of it) used in the mapping cross; leave blank if not available" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	328 <param name="infer_missing" type="boolean" truevalue="--infer-missing" falsevalue="" checked="false"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	329 label="Infer alleles for missing parent"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	330 help="if variant data for either the related or the unrelated parent strain is not available, the tool can try to infer the alleles present in that parent from the allele spectrum found in the mapping sample. Use with caution on carefully filtered variant lists only!" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	331 <param name="contrast_sample" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	332 <expand macro="vaf_unconditional" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	333 <param name="tabfile" type="select"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	334 label="additional per-variant output file"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	335 help="You can either choose to produce a tabular per-variant report, which is useful for fast replotting with different plot settings, or a VCF-like CloudMap-compatibility output that can be used as input for the older CloudMap Hawaiian Variant Mapping tool as an alternative plotting tool.">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	336 <option value="">Do not generate per-variant output</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	337 <option value="-t">Tabular per-variant report</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	338 <option value="--cloudmap -t">CloudMap compatibility output</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	339 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	340 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	341 <when value="rep">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	342 <param name="ifile" type="data" format="tabular,csv"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	343 label="input file with variants to analyze" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	344 <expand macro="seqdict_param" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	345 <param name="tabfile" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	346 <expand macro="hidden_algo_params" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	347 <expand macro="vaf_unconditional" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	348 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	349 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	350 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	351 <when value="VAC">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	352 <conditional name="source">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	353 <param name="inputtype" type="select"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	354 label="data source to use">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	355 <option value="vcf">VCF file of variants (for de-novo mapping)</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	356 <option value="rep">per-variant report file (for remapping a previous analysis)</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	357 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	358 <when value="vcf">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	359 <param name="ifile" type="data" format="vcf"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	360 label="input file with variants to analyze" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	361 <expand macro="seqdict_param" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	362 <expand macro="hidden_vaf_algo_params" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	363 <param name="sample" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	364 label="mapping sample name"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	365 help="the sample to perform mutation mapping for">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	366 <validator type="empty_field" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	367 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	368 <param name="contrast_sample" type="text"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	369 label="name of the contrast sample"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	370 help="the sample that provides contrasting allele composition around the causal variant">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	371 <validator type="empty_field" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	372 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	373 <expand macro="vac_unconditional" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	374 <param name="tabfile" type="select"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	375 label="additional per-variant output file"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	376 help="You can choose to produce a tabular per-variant report, which is useful for fast replotting with different plot settings.">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	377 <option value="">Do not generate per-variant output</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	378 <option value="-t">Tabular per-variant report</option>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	379 </param>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	380 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	381 <when value="rep">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	382 <param name="ifile" type="data" format="tabular,csv"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	383 label="input file with variants to analyze" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	384 <expand macro="seqdict_param" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	385 <param name="tabfile" type="hidden" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	386 <expand macro="hidden_algo_params" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	387 <expand macro="vac_unconditional" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	388 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	389 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	390 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	391 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	392 </inputs>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	393 <outputs>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	394 <data name="ofile" format="tabular"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	395 label="MiModD ${opt.mode} Mapping - binned variant counts for ${on_string}" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	396 <data name="tfile" format="tabular"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	397 label="MiModD ${opt.mode} Mapping - per-variant report for ${on_string}">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	398 <filter>(opt['source']['tabfile'])</filter>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	399 </data>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	400 <data name="pfile" format="pdf"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	401 label="MiModD ${opt.mode} Mapping - linkage plots for ${on_string}">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	402 <filter>(opt['source']['plotopts']['plots'])</filter>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	403 </data>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	404 </outputs>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	405
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	406 <tests>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	407 <test expect_num_outputs="1">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	408 <conditional name="opt">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	409 <param name="mode" value="SVD" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	410 <conditional name="source">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	411 <param name="inputtype" value="vcf" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	412 <conditional name="plotopts">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	413 <param name="plots" value="" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	414 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	415 <param name="ifile" value="a.vcf" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	416 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	417 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	418 <expand macro="test_tabular_out" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	419 </test>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	420 <test expect_num_outputs="2">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	421 <conditional name="opt">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	422 <param name="mode" value="VAF" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	423 <conditional name="source">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	424 <param name="inputtype" value="vcf" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	425 <conditional name="plotopts">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	426 <param name="plots" value="-p" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	427 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	428 <param name="sample" value="ot266" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	429 <param name="related_parent_sample" value="N2" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	430 <param name="ifile" value="a.vcf" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	431 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	432 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	433 <expand macro="test_tabular_out" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	434 <output name="pfile" file="vaf_linkage.pdf" ftype="pdf"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	435 compare="sim_size" delta="100000" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	436 </test>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	437 </tests>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	438
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	439 <help><![CDATA[
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	440 .. class:: infomark
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	441
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	442 What it does
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	443
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	444 This is the most downstream tool in
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	445 `mapping-by-sequencing analysis workflows in MiModD`_.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	446
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	447 It can be used to analyze and visualize the inheritance pattern of variants
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	448 detected and selected with other MiModD tools or as an alternative (and more
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	449 versatile) plotting engine for data generated with `CloudMap`_.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	450
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	451 -------------
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	452
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	453 Usage Modes:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	454
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	455 This tool can be run in one of three different modes depending on the type of
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	456 mapping analysis that should be performed:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	457
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	458 1) Simple Variant Density (SVD) Mapping mode analyzes the density of variants
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	459 along the reference genome by dividing each chromosome into regions of
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	460 user-defined size (bins) and counting the variants found in each bin.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	461
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	462 All variants listed in the input file are analyzed in this mode, which means
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	463 that as input you will typically want to use filtered lists of variants (as
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	464 produced by the VCF Filter tool).
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	465
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	466 The aim of SVD analysis is to identify clusters of variants in an outcrossed
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	467 strain carrying a selectable unknown mutation, which is interpreted as
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	468 linkage between the corresponding genomic region and the unknown mutation.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	469
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	470 This mode corresponds roughly to EMS Variant Density Mapping in CloudMap.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	471
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	472 2) Variant Allele Frequency (VAF) Mapping mode analyzes the inheritance
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	473 pattern in cross-progeny at sites, at which the parents are homozygous for
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	474 different alleles.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	475
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	476 The aim of VAF analysis is to identify clusters of variants with (near)
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	477 homozygous inheritance in a F2 (or later generation) population obtained
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	478 from a cross between a strain carrying a selectable unknown mutation and an
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	479 unrelated mapping strain. Such a cluster is interpreted as linkage between
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	480 the corresponding genomic region and the unknown mutation selected for in
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	481 the F2 generation.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	482
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	483 This mode corresponds roughly to Hawaiian Variant Mapping in CloudMap, but
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	484 can simultaneously take into account non-reference alleles found in either
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	485 parent strain (CloudMap users may think of this as a combined Hawaiian
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	486 Variant and Variant Discovery Mapping analysis).
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	487
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	488 3) Variant Allele Contrast (VAC) Mapping mode analyzes and visualizes the
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	489 divergence between two samples at all sites in the input dataset. It works
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	490 independent of any parent strain information and can be used if you have two
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	491 samples selected for contrary phenotypes, but also with a selected and a
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	492 non-selected sample.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	493
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	494 -------------
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	495
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	496 Input:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	497
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	498 Valid input for this tool are VCF datasets (any such dataset in SVD mode, a
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	499 MiModD-generated multi-sample VCF dataset in VAF and VAC modes) or a tabular
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	500 report as generated by the CloudMap Hawaiian Variant Mapping tool.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	501 Alternatively, the tool can generate (in both modes) its own tabular reports,
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	502 which can be used as input instead of the original VCF dataset, when rerunning
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	503 the tool with different plotting parameters, to reduce analysis time.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	504
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	505 -------------
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	506
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	507 Output:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	508
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	509 The tool produces up to three output files:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	510
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	511 1) a default tabular report of binned variant counts that can be used to plot
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	512 the data with external software such as Excel,
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	513
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	514 2) an optional pdf containing linkage plots, and
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	515
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	516 3) an optional tabular per-variant report, which can be configured to be either
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	517 valid input for the corresponding original CloudMap tool (for users who
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	518 really, really want to continue using CloudMap for plotting) or to be
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	519 reusable in fast reruns of the tool (which can be useful to experiment with
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	520 different plotting parameters).
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	521
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	522 -------------
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	523
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	524 Settings:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	525
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	526 1) Analysis settings
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	527
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	528 bin size to analyze variants in - determines the width of the regions
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	529 along each chromosome, in which variants are counted and analyzed together.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	530
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	531 Several bin sizes can be specified and for each size you will get a
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	532 corresponding results section in the binned variant counts report and a
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	533 linkage histogram plot.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	534
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	535 sample names (in VAF and VAC modes only) - to analyze inheritance
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	536 patterns, the VAF and VAC modes need information about the relationship
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	537 between the samples defined in the input. While VAC mode simply requires
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	538 you to name the two contrasting samples for the analysis, the sample roles
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	539 in VAF mode are a bit more complicated to understand. Specifically:
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	540
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	541 The mapping sample name should be set to the name of the sample for which
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	542 the inheritance pattern is to be analyzed (the pooled progeny population).
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	543
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	544 The name of the related sample should indicate the parent sample that
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	545 carried and brought in the unknown mutation to be mapped (or, alternatively,
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	546 a closely related ancestor).
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	547
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	548 The name of the unrelated sample should be that of the other parent strain
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	549 used in the cross.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	550
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	551 At least one of the parent samples MUST be specified, but if the input
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	552 contains variant information for both parents, they can be analyzed together
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	553 for higher mapping accuracy. If you are reanalyzing a tabular report from a
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	554 previous tool run or from CloudMap, the association between variants and
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	555 samples is already stored in the input dataset and cannot be specified
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	556 again.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	557
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	558 2) Graphical output settings
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	559
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	560 .. class:: warningmark
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	561
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	562 To be able to generate plots, the system running MiModD needs to have the
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	563 statistical programming environment R and its Python interface rpy2
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	564 installed. Disable graphical output if this is not the case.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	565
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	566 y-axes scaling - if you want to override the defaults
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	567
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	568 x-axis scaling - choose preserve relative contig sizes if you want the
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	569 largest chromosome to fit the page width and smaller chromosomes to appear
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	570 according to their relative size or choose *scale each contig to fit the
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	571 plot width* if all chromosomes should exploit the available space
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	572
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	573 span value to be used in calculating the Loess regression line - this
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	574 value determines the degree of smoothing of the regression line through the
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	575 scatterplot data. Information on loess regression and the loess span
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	576 parameter can be found at http://en.wikipedia.org/wiki/Local_regression.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	577
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	578 colors used for plotting - can be selected freely from the offered
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	579 palette. For histogram colors, the list of selected colors will be used to
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	580 provide the colors for the different histograms plotted. If less colors than
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	581 histograms (determined by the number of bin sizes selected) are specified,
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	582 colors from the list will be recycled.
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	583
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	584 .. _CloudMap: https://usegalaxy.org/u/gm2123/p/cloudmap
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	585 .. _mapping-by-sequencing analysis workflows in MiModD: http://mimodd.readthedocs.io/en/latest/nacreousmap.html
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	586 .. _CloudMap-style sequence dictionary: http://mimodd.readthedocs.io/en/latest/fileformats.html#cloudmap-style-sequence-dictionary
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	587
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	588 @HELP_FOOTER@
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	589 ]]></help>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	590 <expand macro="citations" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797 wolma parents: diff changeset	591 </tool>

Mercurial > repos > wolma > mimodd_core

annotate cloudmap.xml @ 2:36b4be01cce4 draft default tip