Mercurial > repos > recetox > recetox_xmsannotator_simple

comparison 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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0:4cf6d71da794 1:fa85bd6fd713
1 <tool id="recetox_xmsannotator_simple" name="xmsannotator - simple" version="deployment"> 1 <tool id="recetox_xmsannotator_simple" name="xmsannotator - simple" version="v2.0">
2 <macros> 2 <macros>
3 <import>recetox_xmsannotator_macros.xml</import> 3 <import>recetox_xmsannotator_macros.xml</import>
4 </macros> 4 </macros>
5 5
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 7
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 Rscript -e 'annotation <- xmsannotator::simple_annotation( 9 Rscript -e 'annotation <- xmsannotator::simple_annotation(
10 data = arrow::read_feather("$peaks"), 10 peaks = arrow::read_feather("$peaks"),
11 adducts = rhdf5::h5read("$adducts", "adducts"),
11 metabolites = rhdf5::h5read("$metabolites", "metabolites"), 12 metabolites = rhdf5::h5read("$metabolites", "metabolites"),
12 mz_tolerance_ppm = as.double($mz_tolerance) 13 mz_tolerance = as.double($mass_tolerance)
13 )' 14 )'
14 -e 'arrow::write_feather(annotation, "$annotation")' 15 -e 'arrow::write_feather(annotation, "$annotation")'
15 ]]></command> 16 ]]></command>
16 17
17 <inputs> 18 <inputs>
18 <expand macro="peaks"/> 19 <param name="peaks" type="data" format="feather" label="Peaks" help="Table of peak intensities."/>
19 <expand macro="metabolites"/> 20 <param name="metabolites" type="data" format="h5" label="Metabolite database"/>
20 <expand macro="mz_tolerance"/> 21 <param name="adducts" type="data" format="h5" label="Adduct database"/>
22
23 <param name="mass_tolerance" type="float" value="10" min="0" label="Mass tolerance [ppm]" help="Mass tolerance in ppm for database matching."/>
21 </inputs> 24 </inputs>
22 25
23 <outputs> 26 <outputs>
24 <expand macro="annotation_output"/> 27 <data format="feather" name="annotation"/>
25 </outputs> 28 </outputs>
26 29
27 <help><![CDATA[]]></help> 30 <help><![CDATA[]]></help>
28 <expand macro="citations"/> 31 <expand macro="citations"/>
29 </tool> 32 </tool>