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annotate xmsannotator_simple.xml @ 2:041052875af0 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit de75adf885d616bbe94c8087d3208a2b5039418e"
author recetox
date Thu, 08 Oct 2020 00:41:12 +0000
parents 97d1619ff23e
children 412d8bb4b54d
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97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
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1 <tool id="xmsannotator_simple" name="xMSannotator (simple)" version="@TOOL_VERSION@+galaxy0">
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2 <macros>
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3 <import>xmsannotator_macros.xml</import>
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4 </macros>
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6 <requirements>
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7 <container type="docker">@DOCKER_IMAGE@</container>
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8 </requirements>
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97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
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10 <command detect_errors="aggressive"><![CDATA[
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11 Rscript -e 'annotation <- xmsannotator::simple_annotation(
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12 peaks = xmsannotator::load_hdf("$peaks", "peaks"),
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13 adducts = xmsannotator::load_hdf("$adducts", "adducts"),
041052875af0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit de75adf885d616bbe94c8087d3208a2b5039418e"
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14 compounds = xmsannotator::load_hdf("$compounds", "compounds"),
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15 mass_tolerance = 1e-6 * $mz_tolerance_ppm
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16 )'
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17 -e 'xmsannotator::save_hdf("$annotation", "annotation", annotation)'
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18 ]]></command>
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20 <inputs>
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21 <expand macro="annotation"/>
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22 </inputs>
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24 <outputs>
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25 <data format="h5" name="annotation"/>
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26 </outputs>
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28 <help><![CDATA[
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29 Annotate the peak intensity table (such as outputted from apLCMS) with metabolites from the metabolite database.
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97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
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31 The annotation process generates all possible metabolite-adduct pairs from the metabolite and adduct databases and matches those pairs to the measured peaks.
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
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32 A metabolite-adduct pair is pronounced as a match to the peak when the difference of their masses are withing some tolerance.
97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
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33 ]]></help>
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35 <expand macro="citations"/>
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36 </tool>