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annotate gcms2isocor.xml @ 2:6ce747c94164 draft

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"planemo upload commit 9297c59dab98c382a39fe24d0b6906e94bf34d07"
author genouest
date Tue, 19 Oct 2021 15:21:18 +0000
parents 6042d557e451
children 4faf831e1960
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1 <tool id="gcms2isocor" name="Conversion GCMS PostRun Analysis to IsoCor" 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 -jar '$__tool_directory__/P2M2WorkflowsTools-assembly-0.1.jar'
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7 #for $input in $input_gcms_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_isocor'
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13 ]]></command>
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14 <inputs>
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15 <param type="data" name="input_gcms_files" multiple="true" format="txt" />
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16 </inputs>
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17 <outputs>
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18 <data name="output_isocor" format="tsv" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input_gcms_files" value="13CPROT1.txt,13CPROT2.txt"/>
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23 <output name="output_isocor" file="input_isocor.tsv"/>
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24 </test>
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25 </tests>
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26 <help><![CDATA[
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27 Convert the GC-MS raw data input files into a unique table suitable as input file for IsoCor.
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29 Processes GCMS files should be exported with the following categories: [Header], [MS Quantitative Results].
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30 GC-MS raw dataset should contains a column "Name" filled with each carbon isotopologue of each fragment considered and a column "Area" filled with the area of the integrated peak.
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31 The name of each fragment must be written exactly as specified in the "Metabolite.dat" file (see https://isocor.readthedocs.io/en/latest/tutorials.html#input-data) to ensure accurate correction with
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32 IsoCor.
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34 Example: the name “ProlineC2C5_TMS_m0” is for the GC-MS fragment m/z 142 (integrated peak) containing the C2-C3-C4-C5 carbon skeleton of proline and 1 TMS derivative. m0 refers to the carbon isotopologue
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35 monitored (m0 for m/z = 142, m1 for m/z = 143, m2 for m/z = 144, m3 for m/z = 145, m4 for m/z = 146).
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36 ]]></help>
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37 </tool>