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annotate MetaRNAseq.xml @ 1:a978d1560ea3 draft

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planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b-dirty
author sblanck
date Thu, 22 Feb 2018 08:39:38 -0500
parents 1024245abc70
children f18413a94742
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1 <tool id="metarnaseq" name="RNA-seq data meta-analysis" version="1.0.0">
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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3 <description>Performs meta-analysis thanks to metaRNAseq</description>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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5 <requirements>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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6 <requirement type="package">bioconductor-affy</requirement>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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7 <requirement type="package">bioconductor-annaffy</requirement>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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8 <requirement type="package">bioconductor-geoquery</requirement>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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9 <requirement type="package">r-venndiagram</requirement>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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10 <requirement type="package">r-jsonlite</requirement>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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11 <requirement type="package">r-metarnaseq</requirement>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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12 <requirement type="package">r-optparse</requirement>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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13 </requirements>
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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15 <stdio>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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16 <exit_code range="1:" />
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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17 <regex match="Warning" source="both" level="warning"/>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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18 </stdio>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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20 <command>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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22 <![CDATA[
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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23 Rscript
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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24 ${__tool_directory__}/MetaRNASeq.R
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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25 --input "#for $input in $inputs# $input;$input.name, #end for#"
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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26 --result $top_table
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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27 --htmloutput $result_html
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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28 --htmloutputpath $result_html.extra_files_path
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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29 --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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30 ]]>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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31 </command>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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33 <inputs>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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34 <param format="tabular" name="inputList" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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35 </inputs>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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37 <outputs>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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38 <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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39 <data format="html" name="diagnostic_html" label="Charts for ${tool.name} on ${on_string}"/>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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40 </outputs>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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42 <tests>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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44 </tests>
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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46 <help>
1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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48 </help>
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1024245abc70 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 5974f806f344dbcc384b931492d7f023bfbbe03b
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50 </tool>