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comparison staramr_search.xml @ 12:aeaa20b96ef2 draft

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"planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/tools/staramr commit 014bea9d3a8d8bda2eebe4dde697b72c776ff158"
author nml
date Sat, 04 Apr 2020 19:27:12 -0400
parents 5f43703968cf
children 2fd4d4c9c5c2
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11:5f43703968cf 12:aeaa20b96ef2
1 <tool id="staramr_search" name="staramr" version="@VERSION@"> 1 <tool id="staramr_search" name="staramr" version="@VERSION@+galaxy1">
2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description> 2 <description>Scans genome assemblies against the ResFinder, PlasmidFinder, and PointFinder databases searching for AMR genes.</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">0.7.1</token> 4 <token name="@VERSION@">0.7.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
15 #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier)) 15 #set $_named_genome = re.sub(r'(\s|\(|\)|\/)', '_', '"{}.fasta"'.format($genome.element_identifier))
16 ln -s '$genome' $_named_genome && 16 ln -s '$genome' $_named_genome &&
17 #set $named_genomes = $named_genomes + ' ' + $_named_genome 17 #set $named_genomes = $named_genomes + ' ' + $_named_genome
18 #end for 18 #end for
19 19
20 #set $excel_proper_extension = '"{}.xlsx"'.format($excel) 20 #set $excel_proper_extension = '"results.xlsx"'
21 ln -s "$excel" $excel_proper_extension && 21 ln -s "$excel" $excel_proper_extension &&
22 22
23 staramr search 23 staramr search
24 24
25 --nprocs "\${GALAXY_SLOTS:-1}" 25 --nprocs "\${GALAXY_SLOTS:-1}"