Mercurial > repos > jpayne > bam_dealer

comparison paired_bam_dealer.xml @ 6:add58a8a67f0 tip

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planemo upload commit b'5e9a6cdf7bbe14678aa83ae2304bde4b6ad2976d\n'-dirty
author jpayne
date Fri, 08 Dec 2017 14:03:09 -0500
parents 55df0d1c6365
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5:55df0d1c6365 6:add58a8a67f0
1 <tool id="paired_bam_dealer" name="Deal out" version="0.1.0"> 1 <tool id="paired_bam_dealer" name="Deal out" version="0.1.0">
2 <description>paired-end reads by alignment or non-alignment to a reference</description> 2 <description>paired-end reads by alignment or non-alignment to a reference</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.5">samtools</requirement> 4 <requirement type="package" version="1.3.1">samtools</requirement>
5 <requirement type="package" version="2.26">bedtools</requirement> 5 <requirement type="package" version="2.26">bedtools</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 bamToFastq -i <(samtools sort -n <(samtools view -u -f 1 -F 12 $input_bam )) 8 bamToFastq -i <(samtools sort -n <(samtools view -u -f 1 -F 12 $input_bam ))
9 -fq $mapped_1 9 -fq $mapped_1