Mercurial > repos > gaelcge > r_signac_galaxy

annotate signac_vlnplot.xml @ 0:6e0b320d8b6a draft default tip

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"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
author gaelcge
date Tue, 02 Aug 2022 19:11:27 +0000
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1 <tool id="signac_vlnplot" name="Violin Plot" version="0.1.0" python_template_version="3.5">
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2 <description> of selected features.</description>
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3 <macros>
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4 <import>signac_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <stdio>
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8 <exit_code range="1:"/>
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9 </stdio>
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10 <command><![CDATA[
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11 Rscript '${__tool_directory__}'/signac-vlnplot.R --signac-object $signac_object --features $features --cols $cols --pt-size $pt_size --group-by $group_by --sort $sort --assay $assay --same-y-lims $same_y_lims --log $log --ncol $ncol --slot $slot --stack $stack --fill-by $fill_by --flip $flip --png-width $png_width --png-height $png_height --output_image_file $vlnplot_file
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12 ]]></command>
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13 <inputs>
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14 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/>
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15 <param type="text" name="features" label="Features (separated by a comma)" optional="false"/>
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16 <param type="text" name="cols" label="Colours" value="NULL" format="txt" multiple="false" optional="false"/>
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17 <param type="float" name="pt_size" value='1' label="Point size" optional="true"/>
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18 <param type="text" name="group_by" value='ident' label="Group by"/>
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19 <param type="boolean" name="sort" value='false' label="Sort"/>
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20 <param type="text" name="assay" value='NULL' format="txt" label="Assay"/>
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21 <!-- <param type="text" name="split_by" value='NULL' label="A split the violin plots by"/> -->
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22 <param type="boolean" name="same_y_lims" value='false' label="Same y limits"/>
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23 <param type="boolean" name="log" value='false' label="Plot on log scale"/>
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24 <param type="integer" name="ncol" value='3' label="Number of columns"/>
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25 <param type="text" name="slot" value='data' label="Data slot"/>
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26 <!-- <param type="boolean" name="split_plot" value='false' label="Plot each group of the split violin plots by multiple or single violin shapes"/> -->
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27 <param type="boolean" name="stack" value='false' label="Horizontally stack plots for each feature"/>
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28 <param type="select" name="fill_by" label="Color violins/ridges based on either 'feature' or 'ident'">
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29 <option value="feature">feature</option>
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30 <option value="ident">ident</option>
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31 </param>
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32 <param type="boolean" name="flip" value='false' label="flip plot orientation (identities on x-axis)"/>
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33 <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.'/>
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34 <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/>
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35 </inputs>
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36 <outputs>
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37 <data name="vlnplot_file" format="png" from_work_dir="Vlnplot.png" label="Signac.vlnplot.png"/>
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38 </outputs>
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39 <help><![CDATA[
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40 This tool creates a violin plot and saves it as a .png file.
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41 ]]></help>
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42 </tool>