Mercurial > repos > drosofff > msp_sr_bowtie_parser

comparison sRbowtieParser.xml @ 16:bfeaf4415eba draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie_parser commit 30a73e24eabb05f9d46150fd03471ff853579ad2-dirty
author mvdbeek
date Mon, 18 Apr 2016 09:41:34 -0400
parents a39761c27e77
children 7b5e0fba8e74
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15:a39761c27e77 16:bfeaf4415eba
1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.5"> 1 <tool id="sRbowtieParser" name="Parse items in sRbowtie alignment" version="1.0.6">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.12.7">bowtie</requirement> 4 <requirement type="package" version="0.12.7">bowtie</requirement>
5 <requirement type="package" version="0.7.7">pysam</requirement> 5 <requirement type="package" version="0.7.7">pysam</requirement>
6 <requirement type="package" version="1.9">numpy</requirement> 6 <requirement type="package" version="1.9">numpy</requirement>
7 </requirements> 7 </requirements>
8 <command interpreter="python"> 8 <command>
9 sRbowtieParser.py 9 python sRbowtieParser.py
10 #if $refGenomeSource.genomeSource == "history": 10 #if $refGenomeSource.genomeSource == "history":
11 --IndexSource $refGenomeSource.ownFile 11 --IndexSource $refGenomeSource.ownFile
12 --ExtractDirective fastaSource 12 --ExtractDirective fastaSource
13 #else: 13 #else:
14 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] 14 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
25 #for $i in $refGenomeSource.input_list 25 #for $i in $refGenomeSource.input_list
26 $i.ext 26 $i.ext
27 #end for 27 #end for
28 --alignmentLabel 28 --alignmentLabel
29 #for $i in $refGenomeSource.input_list 29 #for $i in $refGenomeSource.input_list
30 "$i.name" 30 "$i.element_identifier"
31 #end for 31 #end for
32 32
33 </command> 33 </command>
34 <inputs> 34 <inputs>
35 <conditional name="refGenomeSource"> 35 <conditional name="refGenomeSource">