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comparison sRbowtie.xml @ 7:3d5bd42097d7 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit cf30b4fab90cf7910bb2900a05b85ca3344aae59
author artbio
date Tue, 15 Nov 2022 00:44:57 +0000
parents e4a05086ea02
children
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6:e4a05086ea02 7:3d5bd42097d7
1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.2.0"> 1 <tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.3.0">
2 <description>for small RNA short reads</description> 2 <description>for small RNA short reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3.1">bowtie</requirement> 4 <requirement type="package" version="1.3.1">bowtie</requirement>
5 <requirement type="package" version="1.14">samtools</requirement> 5 <requirement type="package" version="1.14">samtools</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if $refGenomeSource.genomeSource == "history": 8 #if $refGenomeSource.genomeSource == "history":
9 bowtie-build -f $refGenomeSource.ownFile genome 1>/dev/null && 9 bowtie-build --threads \${GALAXY_SLOTS:-4} -f $refGenomeSource.ownFile genome 1>/dev/null &&
10 ln -s -f '$refGenomeSource.ownFile' genome.fa && 10 ln -s -f '$refGenomeSource.ownFile' genome.fa &&
11 #set index_path = 'genome' 11 #set index_path = 'genome'
12 #else: 12 #else:
13 #set index_path = $refGenomeSource.index.fields.path 13 #set index_path = $refGenomeSource.index.fields.path
14 #end if 14 #end if