Mercurial > repos > drosofff > msp_sr_bowtie_parser

comparison sRbowtieParser.xml @ 1:f5388910d083 draft

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author mvdbeek
date Sun, 29 Mar 2015 11:27:33 -0400
parents 3a510730e3fc
children 70193ce0540e
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0:3a510730e3fc 1:f5388910d083
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="0.1.18">samtools</requirement> 5 <requirement type="package" version="0.1.18">samtools</requirement>
6 <requirement type="package" version="0.7.7">pysam</requirement> 6 <requirement type="package" version="0.7.7">pysam</requirement>
7 <requirement type="package" version="1.9">numpy</requirement>
8 <requirement type="package" version="0.14">scipy</requirement>
7 </requirements> 9 </requirements>
8 <parallelism method="basic"></parallelism>
9 <command interpreter="python"> 10 <command interpreter="python">
10 sRbowtieParser.py 11 sRbowtieParser.py
11 #if $refGenomeSource.genomeSource == "history": 12 #if $refGenomeSource.genomeSource == "history":
12 --IndexSource $refGenomeSource.ownFile 13 --IndexSource $refGenomeSource.ownFile
13 --ExtractDirective fastaSource 14 --ExtractDirective fastaSource
71 **It is thus essential that input datasets are appropriately renamed** 72 **It is thus essential that input datasets are appropriately renamed**
72 73
73 **it is preferable that you do not put any space in this input dataset names. You may edit these names in the history** 74 **it is preferable that you do not put any space in this input dataset names. You may edit these names in the history**
74 75
75 </help> 76 </help>
76 <test> 77 <tests>
78 <test>
77 <param name="genomeSource" value="history" /> 79 <param name="genomeSource" value="history" />
78 <param name="ownFile" value ="dme-mir-v20" ftype="fasta" /> 80 <param name="ownFile" value ="dme-mir-v20" ftype="fasta" />
79 <param name="input_list" value="matchedSample_1, matchedSample_2" ftype="tabular" /> 81 <param name="input_list" value="matchedSample_1,matchedSample_2" ftype="tabular" />
80 <param name="polarity" value="forward" /> 82 <param name="polarity" value="forward" />
81 <output name="output" ftype="tabular" value="Read_Count_Lists.tab" /> 83 <output name="output" ftype="tabular" file="Read_Count_Lists.tab" />
82 </test> 84 </test>
83 85 </tests>
84 </tool> 86 </tool>
85 87