Mercurial > repos > genouest > openlabcds2csv

comparison openlabcds2csv.xml @ 0:9072a2d2178b draft

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"planemo upload commit c24cf4eadc45f2915f24cae2940c81c12dd3aab4"
author genouest
date Fri, 29 Oct 2021 13:59:09 +0000
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1 <tool id="openlabcds2csv" name="Converting multiple OpenLabCDS Text Files to a CSV summary file" version="0.1.0" profile="21.05">
2 <requirements>
3 <requirement type="package" version="8.0.121">openjdk</requirement>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 java -cp '$__tool_directory__/P2M2WorkflowsTools-assembly-0.1.4.jar' fr.inrae.metabolomics.p2m2.OpenLabCDS2CsvCommand
7 #for $input in $input_openlabscds_files
8 #if $input
9 $input
10 #end if
11 #end for
12 --out '$output_csv' --column '$column'
13 ]]></command>
14 <inputs>
15 <param type="data" name="input_openlabscds_files" multiple="true" format="txt" />
16 <param type="select" name="column" label="target column to build as summary">
17 <option value="RetTime">RetTime</option>
18 <option value="Type">Type</option>
19 <option value="ISTD">ISTD</option>
20 <option value="Area" selected="true">Area</option>
21 <option value="Amt/Area">Amt/Area</option>
22 <option value="Amount">Amount</option>
23 <option value="Grp">Grp</option>
24 </param>
25 </inputs>
26 <outputs>
27 <data name="output_csv" format="csv" />
28 </outputs>
29 <tests>
30 <test>
31 <param name="input_openlabscds_files" value="Report_Ex1.txt,Report_Ex2.txt,Report_Ex3.txt"/>
32 <param name="column" value="Area"/>
33 <output name="output_csv" file="Results.csv"/>
34 </test>
35 </tests>
36 <help><![CDATA[
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)
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)
39 ]]></help>
40 </tool>