Mercurial > repos > genouest > gcms2isocor

comparison 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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1:6042d557e451 2:6ce747c94164
22 <param name="input_gcms_files" value="13CPROT1.txt,13CPROT2.txt"/> 22 <param name="input_gcms_files" value="13CPROT1.txt,13CPROT2.txt"/>
23 <output name="output_isocor" file="input_isocor.tsv"/> 23 <output name="output_isocor" file="input_isocor.tsv"/>
24 </test> 24 </test>
25 </tests> 25 </tests>
26 <help><![CDATA[ 26 <help><![CDATA[
27 Conversion from GCMS PostRun Analysis to Isocore. 27 Convert the GC-MS raw data input files into a unique table suitable as input file for IsoCor.
28 Processes GCMS files with the following categories: Header, MS Quantitative Results. 28
29 Processes GCMS files should be exported with the following categories: [Header], [MS Quantitative Results].
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.
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
32 IsoCor.
33
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
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).
29 ]]></help> 36 ]]></help>
30 </tool> 37 </tool>