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annotate MetaRNAseq.xml @ 29:102e4ef8fed2 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 808ffb34e11a74cd2396e32868ea56f7ce8d83ff
author sblanck
date Thu, 21 Jun 2018 07:57:16 -0400
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1 <tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.1.0">
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3 <description>Performs meta-analysis thanks to metaRNAseq</description>
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5 <requirements>
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6 <requirement type="package">bioconductor-affy</requirement>
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7 <requirement type="package">bioconductor-annaffy</requirement>
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8 <requirement type="package">bioconductor-geoquery</requirement>
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9 <requirement type="package">r-venndiagram</requirement>
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10 <requirement type="package">r-jsonlite</requirement>
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11 <requirement type="package">r-metarnaseq</requirement>
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12 <requirement type="package">r-optparse</requirement>
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13 <requirement type="package" version="1.3.3">r-upsetr</requirement>
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14 </requirements>
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16 <stdio>
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17 <exit_code range="1:" />
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18 <regex match="Warning" source="both" level="warning"/>
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19 </stdio>
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21 <command>
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23 <![CDATA[
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24 Rscript
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25 ${__tool_directory__}/MetaRNASeq.R
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26 --input "#for $s in $studies:
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27 ${s.input};${s.input.name};${s.nbreplicates},
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28 #end for
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29 "
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30 --fdr $fdr
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31 --result $top_table
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32 --htmloutput $result_html
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33 --htmloutputpath $result_html.extra_files_path
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34 --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html
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35 ]]>
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37 </command>
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39 <inputs>
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40 <repeat name="studies" title="Study results" min="2" default="2" help="DESeq2 Result file and number of replicate of the study">
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41 <param format="tabular" name="input" multiple="false" type="data" optional="false" label="DESeq2 result file" help="Must have the same number of row in each study"/>
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42 <param name="nbreplicates" type="integer" value="10" label="Number of replicates" help="Number of replicates of the study"/>
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43 </repeat>
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44 <param name="fdr" type="float" value="0.05" label="FDR" min="0" max="1" help="adjusted p-value threshold to be declared differentially expressed"/>
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45 </inputs>
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48 <outputs>
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49 <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
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50 <data format="html" name="result_html" label="Charts for ${tool.name} on ${on_string}"/>
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51 </outputs>
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53 <tests>
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55 </tests>
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57 <help>
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59 </help>
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61 </tool>