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comparison bam2wig.xml @ 6:e994caf2503d

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Lance's updates
author nilesh
date Wed, 02 Oct 2013 02:09:28 -0400
parents dc3b3b88fbab
children bc65a465caed
comparison
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1:dc3b3b88fbab 6:e994caf2503d
1 <tool id="bam2wig" name="BAM to Wiggle"> 1 <tool id="bam2wig" name="BAM to Wiggle">
2 <description> 2 <description>
3 converts all types of RNA-seq data from .bam to .wig 3 converts all types of RNA-seq data from .bam to .wig
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.15.1">R</requirement>
7 <requirement type="package" version="0.1.18">samtools</requirement>
8 <requirement type="package" version="2.3.7">rseqc</requirement> 6 <requirement type="package" version="2.3.7">rseqc</requirement>
9 </requirements> 7 </requirements>
10 <command interpreter="python"> 8 <command interpreter="python">
11 samtoolshelper.py /home/nilesh/RSeQC-2.3.3/scripts/bam2wig.py -i $input -s $chromsize -o outfile 9 samtoolshelper.py bam2wig.py -i $input -s $chromsize -o outfile
12 10
13 #if str($strand_type.strand_specific) == "pair" 11 #if str($strand_type.strand_specific) == "pair"
14 -d 12 -d
15 #if str($strand_type.pair_type) == "sd" 13 #if str($strand_type.pair_type) == "sd"
16 '1++,1--,2+-,2-+' 14 '1++,1--,2+-,2-+'