Mercurial > repos > workflow4metabolomics > skyline2isocor

annotate skyline2isocor.xml @ 0:d45fffedc467 draft

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planemo upload for repository https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m commit 23cfca443338f5ae8eed54b44a5b0d7b02563334
author workflow4metabolomics
date Tue, 19 Mar 2024 14:49:27 +0000
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d45fffedc467 planemo upload for repository https://github.com/MetaboHUB-MetaToul-FluxoMet/tools_w4m commit 23cfca443338f5ae8eed54b44a5b0d7b02563334
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1 <tool id='skyline2isocor' name='Skyline2Isocor: converting skyling outputs into IsoCor inputs' version='@TOOL_VERSION@+galaxy0' profile='20.5'>
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2 <macros>
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3 <token name='@TOOL_VERSION@'>0.3.0</token>
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4 </macros>
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5 <requirements>
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6 <requirement type='package' version='@TOOL_VERSION@'>skyline2isocor</requirement>
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7 </requirements>
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8 <command detect_errors='exit_code'><![CDATA[
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9 skyline2isocor -i '$skyline_output' -o '$isocor_input' > '$stdout' 2> '$stderr'
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10 ]]></command>
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11 <inputs>
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12 <param type='data' format='tabular, txt' name='skyline_output' label='Skyline output file' help='Skyline output to convert'/>
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13 </inputs>
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14 <outputs>
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15 <data format='txt' name='stdout' label='Log'/>
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16 <data format='txt' name='stderr' label='Error log' />
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17 <data format='tabular,txt' name='isocor_input' label='IsoCor input file' />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name='skyline_output' value='skyline_output.csv' />
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22 <output name='isocor_input' value='test_output.tsv' />
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23 </test>
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24 </tests>
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25 <help><![CDATA[
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26 Preparing skyline output data for use in IsoCor software for natural abundance isotope correction. Can be directly linked to Isocor in a workflow.
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27 Input is the skyline output. Necessary columns: File Name, Molecule Name, Product Adduct, Total Area.
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28 ]]></help>
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29 <citations>
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30 <citation type='bibtex'>
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31 @misc{
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32 githubskyline2isocor,
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33 author = {Le Gregam, Loic},
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34 year = {2024},
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35 title = {Skyline2IsoCor,
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36 }
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37 </citation>
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38 </citations>
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39 </tool>