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"planemo upload commit efc6f0fdf414834e1275781106dcfe291b7ffd0a"
author genouest
date Fri, 29 Oct 2021 14:23:46 +0000
parents 9072a2d2178b
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1 <tool id="openlabcds2csv" name="Converting multiple OpenLabCDS Text Files to a CSV summary file" version="0.1.0" profile="20.09">
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2 <requirements>
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3 <requirement type="package" version="8.0.121">openjdk</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 java -cp '$__tool_directory__/P2M2WorkflowsTools-assembly-0.1.4.jar' fr.inrae.metabolomics.p2m2.OpenLabCDS2CsvCommand
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7 #for $input in $input_openlabscds_files
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8 #if $input
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9 $input
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10 #end if
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11 #end for
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12 --out '$output_csv' --column '$column'
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13 ]]></command>
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14 <inputs>
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15 <param type="data" name="input_openlabscds_files" multiple="true" format="txt" />
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16 <param type="select" name="column" label="target column to build as summary">
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17 <option value="RetTime">RetTime</option>
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18 <option value="Type">Type</option>
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19 <option value="ISTD">ISTD</option>
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20 <option value="Area" selected="true">Area</option>
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21 <option value="Amt/Area">Amt/Area</option>
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22 <option value="Amount">Amount</option>
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23 <option value="Grp">Grp</option>
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24 </param>
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25 </inputs>
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26 <outputs>
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27 <data name="output_csv" format="csv" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input_openlabscds_files" value="Report_Ex1.txt,Report_Ex2.txt,Report_Ex3.txt"/>
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32 <param name="column" value="Area"/>
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33 <output name="output_csv" file="Results.csv"/>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 Get multiple "Internal Standard Report" from the OpenLabCDS software where are describe a list of compound in format row (columns : RetTime Type ISTD Area Amt/Area Amount Grp Name)
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38 The converter creates a summary that contains a header (a list of compounds) and a list of "Sample name" with associated values ​​for a target column (RetTime,Type,ISTD,Area,Amt/Area,Amount,Grp,Name)
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39 ]]></help>
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40 </tool>