Mercurial > repos > gaelcge > r_signac_galaxy
comparison signac_vlnplot.xml @ 0:6e0b320d8b6a draft default tip
"planemo upload commit dc808171975d0012e25bd7b32adc7a5a5c56a145-dirty"
| author | gaelcge |
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| date | Tue, 02 Aug 2022 19:11:27 +0000 |
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| -1:000000000000 | 0:6e0b320d8b6a |
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| 1 <tool id="signac_vlnplot" name="Violin Plot" version="0.1.0" python_template_version="3.5"> | |
| 2 <description> of selected features.</description> | |
| 3 <macros> | |
| 4 <import>signac_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <stdio> | |
| 8 <exit_code range="1:"/> | |
| 9 </stdio> | |
| 10 <command><![CDATA[ | |
| 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 | |
| 12 ]]></command> | |
| 13 <inputs> | |
| 14 <param type="data" name="signac_object" label="Signac object." format="rdata" multiple="false" optional="false"/> | |
| 15 <param type="text" name="features" label="Features (separated by a comma)" optional="false"/> | |
| 16 <param type="text" name="cols" label="Colours" value="NULL" format="txt" multiple="false" optional="false"/> | |
| 17 <param type="float" name="pt_size" value='1' label="Point size" optional="true"/> | |
| 18 <param type="text" name="group_by" value='ident' label="Group by"/> | |
| 19 <param type="boolean" name="sort" value='false' label="Sort"/> | |
| 20 <param type="text" name="assay" value='NULL' format="txt" label="Assay"/> | |
| 21 <!-- <param type="text" name="split_by" value='NULL' label="A split the violin plots by"/> --> | |
| 22 <param type="boolean" name="same_y_lims" value='false' label="Same y limits"/> | |
| 23 <param type="boolean" name="log" value='false' label="Plot on log scale"/> | |
| 24 <param type="integer" name="ncol" value='3' label="Number of columns"/> | |
| 25 <param type="text" name="slot" value='data' label="Data slot"/> | |
| 26 <!-- <param type="boolean" name="split_plot" value='false' label="Plot each group of the split violin plots by multiple or single violin shapes"/> --> | |
| 27 <param type="boolean" name="stack" value='false' label="Horizontally stack plots for each feature"/> | |
| 28 <param type="select" name="fill_by" label="Color violins/ridges based on either 'feature' or 'ident'"> | |
| 29 <option value="feature">feature</option> | |
| 30 <option value="ident">ident</option> | |
| 31 </param> | |
| 32 <param type="boolean" name="flip" value='false' label="flip plot orientation (identities on x-axis)"/> | |
| 33 <param type="integer" name="png_width" value='1000' label="Figure width" help='Width of png in pixels.'/> | |
| 34 <param type="integer" name="png_height" value='1000' label="Figure height" help='Height of png in pixels.'/> | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data name="vlnplot_file" format="png" from_work_dir="Vlnplot.png" label="Signac.vlnplot.png"/> | |
| 38 </outputs> | |
| 39 <help><![CDATA[ | |
| 40 This tool creates a violin plot and saves it as a .png file. | |
| 41 ]]></help> | |
| 42 </tool> |