Mercurial > repos > genouest > gcms2isocor
annotate gcms2isocor.xml @ 3:4faf831e1960 draft default tip
"planemo upload commit ce164ef16ce1fc3459dc240009ca74dee1b9e005"
author | genouest |
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date | Wed, 20 Oct 2021 12:41:59 +0000 |
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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="tabular" /> |
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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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28 |
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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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33 |
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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> |