Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 28:c1ae0c9ad7d1 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86-dirty
author drosofff
date Sun, 02 Jul 2017 12:22:16 -0400
parents 2578aea69626
children 04685a1b3de1
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27:2578aea69626 28:c1ae0c9ad7d1
4 <requirement type="package" version="1.2">bowtie</requirement> 4 <requirement type="package" version="1.2">bowtie</requirement>
5 <requirement type="package" version="1.4.1">samtools</requirement> 5 <requirement type="package" version="1.4.1">samtools</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if str($refGenomeSource.genomeSource) == "history": 8 #if str($refGenomeSource.genomeSource) == "history":
9 bowtie-build -f '$refGenomeSource.ownFile' local_index && 9 bowtie-build -f $refGenomeSource.ownFile local_index &&
10 #else: 10 #else:
11 ln -f -s '$refGenomeSource.index.fields.path' local_index && 11 ln -f -s $refGenomeSource.index.fields.path local_index &&
12 #end if 12 #end if
13 #if $input.extension == "fasta": 13 #if $input.extension == "fasta":
14 #set format = "-f" 14 #set format = "-f"
15 #elif $input.extension == "fastq": 15 #elif $input.extension == "fastq":
16 #set format = "-q" 16 #set format = "-q"