Mercurial > repos > workflow4metabolomics > gcms2isocor
comparison 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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| -1:000000000000 | 0:d306f2871f03 |
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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"> | |
| 2 <macros> | |
| 3 <token name="@TOOL_VERSION@">0.2.1</token> | |
| 4 <token name="@VERSION_SUFFIX@">0</token> | |
| 5 </macros> | |
| 6 <requirements> | |
| 7 <container type="docker" >inraep2m2/p2m2tools:@TOOL_VERSION@</container> | |
| 8 </requirements> | |
| 9 <command detect_errors="exit_code"><![CDATA[ | |
| 10 p2m2tools fr.inrae.metabolomics.p2m2.command.GCMS2IsocorCommand | |
| 11 #for $input in $input_gcms_files | |
| 12 '$input' | |
| 13 #end for | |
| 14 --out '$output_isocor' | |
| 15 ]]></command> | |
| 16 <inputs> | |
| 17 <param type="data" name="input_gcms_files" multiple="true" format="txt" /> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data name="output_isocor" format="tabular" /> | |
| 21 </outputs> | |
| 22 <tests> | |
| 23 <test> | |
| 24 <param name="input_gcms_files" value="13CPROT1.txt,13CPROT2.txt"/> | |
| 25 <output name="output_isocor" file="input_isocor.tsv" ftype="tabular"/> | |
| 26 </test> | |
| 27 </tests> | |
| 28 <help><![CDATA[ | |
| 29 Convert the GC-MS raw data input files into a unique table suitable as input file for IsoCor. | |
| 30 | |
| 31 Processes GCMS files should be exported with the following categories: [Header], [MS Quantitative Results]. | |
| 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. | |
| 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 | |
| 34 IsoCor. | |
| 35 | |
| 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 | |
| 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). | |
| 38 ]]></help> | |
| 39 <citations> | |
| 40 <citation type="doi">10.15454/1I9PET</citation> | |
| 41 <citation type="doi">10.3389/fpls.2022.885051</citation> | |
| 42 </citations> | |
| 43 </tool> |