Mercurial > repos > recetox > xmsannotator_advanced

comparison xmsannotator_advanced.xml @ 1:477d579f475b draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit f92295d389582c7aefc9ad82762248ba1058a667"
author recetox
date Thu, 24 Sep 2020 07:23:25 +0000
parents 60aec5c0e1ea
children 3bdef6d114fd
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0:60aec5c0e1ea 1:477d579f475b
3 <import>xmsannotator_macros.xml</import> 3 <import>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="exit_code"><![CDATA[
9 #set expected_adducts = ['"{}"'.format($i.adduct) for $i in $scoring.expected_adducts] 9 #set expected_adducts = ['"{}"'.format($i.adduct) for $i in $scoring.expected_adducts]
10 #set expected_adducts = "c(" + ', '.join($expected_adducts) + ")" 10 #set expected_adducts = "c(" + ', '.join($expected_adducts) + ")"
11 11
12 Rscript -e 'annotation <- xmsannotator::advanced_annotation( 12 Rscript -e 'annotation <- xmsannotator::advanced_annotation(
13 peaks = rhdf5::h5read("$peaks", "peaks"), 13 peaks = rhdf5::h5read("$peaks", "peaks"),