Mercurial > repos > drosofff > msp_sr_bowtie_parser
comparison sRbowtieParser.xml @ 16:bfeaf4415eba draft
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"> |