Mercurial > repos > recetox > recetox_xmsannotator_simple

annotate recetox_xmsannotator_simple.xml @ 1:fa85bd6fd713 draft

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"planemo upload commit e434c430917b52ef21b96f0231663c1f1dda34f9-dirty"
author recetox
date Thu, 17 Sep 2020 08:39:26 +0000
parents 4cf6d71da794
children c72233720bdc
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1 <tool id="recetox_xmsannotator_simple" name="xmsannotator - simple" version="v2.0">
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2 <macros>
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3 <import>recetox_xmsannotator_macros.xml</import>
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4 </macros>
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6 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 Rscript -e 'annotation <- xmsannotator::simple_annotation(
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10 peaks = arrow::read_feather("$peaks"),
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11 adducts = rhdf5::h5read("$adducts", "adducts"),
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12 metabolites = rhdf5::h5read("$metabolites", "metabolites"),
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13 mz_tolerance = as.double($mass_tolerance)
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14 )'
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15 -e 'arrow::write_feather(annotation, "$annotation")'
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16 ]]></command>
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18 <inputs>
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19 <param name="peaks" type="data" format="feather" label="Peaks" help="Table of peak intensities."/>
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20 <param name="metabolites" type="data" format="h5" label="Metabolite database"/>
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21 <param name="adducts" type="data" format="h5" label="Adduct database"/>
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23 <param name="mass_tolerance" type="float" value="10" min="0" label="Mass tolerance [ppm]" help="Mass tolerance in ppm for database matching."/>
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24 </inputs>
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26 <outputs>
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27 <data format="feather" name="annotation"/>
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28 </outputs>
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30 <help><![CDATA[]]></help>
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31 <expand macro="citations"/>
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32 </tool>