Mercurial > repos > recetox > xmsannotator_advanced

comparison xmsannotator_advanced.xml @ 7:53246490912c draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit b99706e26938905c4d75763e3041f69fba4bff71"
author recetox
date Fri, 26 Feb 2021 09:05:21 +0000
parents fff8d90068cd
children fbe3edd0a06e
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6:fff8d90068cd 7:53246490912c
1 <tool id="xmsannotator_advanced" name="xMSannotator (advanced)" version="@TOOL_VERSION@+galaxy3"> 1 <tool id="xmsannotator_advanced" name="xMSannotator (advanced)" version="@TOOL_VERSION@+galaxy4">
2 <macros> 2 <macros>
3 <import>xmsannotator_macros.xml</import> 3 <import>xmsannotator_macros.xml</import>
4 </macros> 4 </macros>
5 5
6 <requirements> 6 <requirements>
7 <container type="docker">@DOCKER_IMAGE@</container> 7 <container type="docker">@DOCKER_IMAGE@</container>
8 </requirements> 8 </requirements>
9 9
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 Rscript $wrapper 11 Rscript -e "n_workers <- \${GALAXY_SLOTS:-1}" -e "source('${wrapper}')"
12 ]]></command> 12 ]]></command>
13 13
14 <configfiles> 14 <configfiles>
15 <configfile name="wrapper"><![CDATA[ 15 <configfile name="wrapper"><![CDATA[
16 library(xmsannotator) 16 library(xmsannotator)
34 #end if 34 #end if
35 #if $scoring.boost_compounds 35 #if $scoring.boost_compounds
36 boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds}"), 36 boost_compounds = load_boost_compounds_csv("${scoring.boost_compounds}"),
37 #end if 37 #end if
38 redundancy_filtering = $scoring.redundancy_filtering, 38 redundancy_filtering = $scoring.redundancy_filtering,
39 n_workers = \${GALAXY_SLOTS:-1} 39 n_workers = n_workers
40 ) 40 )
41 41
42 save_parquet(data = annotation, file = "${annotation_parquet}") 42 save_parquet(data = annotation, file = "${annotation_parquet}")
43 ]]></configfile> 43 ]]></configfile>
44 </configfiles> 44 </configfiles>