Mercurial > repos > workflow4metabolomics > gcms2isocor
annotate gcms2isocor.xml @ 0:d306f2871f03 draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
| author | workflow4metabolomics |
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| date | Thu, 11 Apr 2024 16:09:07 +0000 |
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| rev | line source |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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1 <tool id="gcms2isocor" name="Conversion GCMS PostRun Analysis to IsoCor format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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2 <macros> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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3 <token name="@TOOL_VERSION@">0.2.1</token> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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4 <token name="@VERSION_SUFFIX@">0</token> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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5 </macros> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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6 <requirements> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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7 <container type="docker" >inraep2m2/p2m2tools:@TOOL_VERSION@</container> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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8 </requirements> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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9 <command detect_errors="exit_code"><![CDATA[ |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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10 p2m2tools fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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11 #for $input in $input_gcms_files |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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12 '$input' |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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13 #end for |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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14 --out '$output_isocor' |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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15 ]]></command> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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16 <inputs> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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17 <param type="data" name="input_gcms_files" multiple="true" format="txt" /> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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18 </inputs> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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19 <outputs> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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20 <data name="output_isocor" format="tabular" /> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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21 </outputs> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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22 <tests> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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23 <test> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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24 <param name="input_gcms_files" value="13CPROT1.txt,13CPROT2.txt"/> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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25 <output name="output_isocor" file="input_isocor.tsv" ftype="tabular"/> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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26 </test> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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27 </tests> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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28 <help><![CDATA[ |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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29 Convert the GC-MS raw data input files into a unique table suitable as input file for IsoCor. |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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30 |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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31 Processes GCMS files should be exported with the following categories: [Header], [MS Quantitative Results]. |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
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32 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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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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33 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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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
workflow4metabolomics
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34 IsoCor. |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
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35 |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
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36 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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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
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37 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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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
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38 ]]></help> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
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39 <citations> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
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40 <citation type="doi">10.15454/1I9PET</citation> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
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41 <citation type="doi">10.3389/fpls.2022.885051</citation> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
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42 </citations> |
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d306f2871f03
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/gcms2isocor/ commit 9b1b444439a43f4b5dd97e51650fc94f7a66b2e7
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43 </tool> |