Mercurial > repos > iuc > scater_plot_dist_scatter

annotate scater-plot-dist-scatter.xml @ 1:86c3ee9d9f49 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
author iuc
date Tue, 03 Sep 2019 14:21:22 -0400
parents ff695f98c32c
children dcda8e123809
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ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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1 <tool id="scater_plot_dist_scatter" name="Scater: plot library QC" version="@TOOL_VERSION@">
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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2 <description>Create plots to visualise library size, feature counts and mito gene expression</description>
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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3 <macros>
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4 <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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5 </macros>
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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6 <expand macro="requirements">
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86c3ee9d9f49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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7 <requirement type="package" version="0.2.2">r-ggpubr</requirement>
86c3ee9d9f49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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8 <requirement type="package" version="1.0.0">r-scales</requirement>
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ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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9 </expand>
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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10 <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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11 Rscript '$__tool_directory__/scater-plot-dist-scatter.R'
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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12 -i '$input_loom'
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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13 -o '$output_plot'
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86c3ee9d9f49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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14 $plot_log
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ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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15 ]]></command>
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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16 <inputs>
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17 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
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18 <param name="plot_log" type="boolean" truevalue="--log-scale" falsevalue="" label="Plot on log scale" help="Recommended for large datasets" />
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19 </inputs>
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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20 <outputs>
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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21 <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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22 </outputs>
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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23 <tests>
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24 <test>
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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25 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
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26 <param name="plot_log" value="false"/>
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27 <output name="output_plot" file="scater_reads_genes_dist.pdf" compare="sim_size" />
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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28 </test>
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29 <test>
86c3ee9d9f49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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30 <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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31 <param name="plot_log" value="true"/>
86c3ee9d9f49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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32 <output name="output_plot" file="scater_reads_genes_dist_log.pdf" compare="sim_size" />
86c3ee9d9f49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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33 </test>
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34 </tests>
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35 <help><![CDATA[
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36 Plot distribution of reads and features for single-cell RNA-seq analysis using Scater.
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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37 ]]></help>
ff695f98c32c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
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38 <expand macro="citations" />
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39 </tool>