Mercurial > repos > iuc > scater_plot_dist_scatter

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 9961b5acbf9081f10e14bc272406b36854fa2924"
author iuc
date Mon, 08 Nov 2021 11:59:02 +0000
parents 13ff6276ba1b
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13ff6276ba1b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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1 <tool id="scater_plot_dist_scatter" name="Scater: plot library QC" version="@TOOL_VERSION@" profile="@PROFILE@">
13ff6276ba1b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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2 <description>to visualise library size, feature counts and mito gene expression</description>
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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6 </macros>
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7 <expand macro="requirements">
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13ff6276ba1b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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8 <requirement type="package" version="0.4.0">r-ggpubr</requirement>
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9 <requirement type="package" version="1.1.1">r-scales</requirement>
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10 </expand>
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11 <command detect_errors="exit_code"><![CDATA[
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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12 Rscript '$__tool_directory__/scater-plot-dist-scatter.R'
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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13 -i '$input_loom'
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14 -o '$output_plot'
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15 $plot_log
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16 ]]></command>
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17 <inputs>
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18 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
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19 <param name="plot_log" type="boolean" truevalue="--log-scale" falsevalue="" label="Plot on log scale" help="Recommended for large datasets" />
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20 </inputs>
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21 <outputs>
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22 <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
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27 <param name="plot_log" value="false"/>
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28 <output name="output_plot" file="scater_reads_genes_dist.pdf" compare="sim_size" />
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29 </test>
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30 <test>
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31 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
86c3ee9d9f49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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32 <param name="plot_log" value="true"/>
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33 <output name="output_plot" file="scater_reads_genes_dist_log.pdf" compare="sim_size" />
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 Plot distribution of reads and features for single-cell RNA-seq analysis using Scater.
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38 ]]></help>
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39 <expand macro="citations" />
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40 </tool>