Mercurial > repos > jpayne > bam_dealer

comparison paired_bam_dealer.xml @ 3:b7bbe08d50df

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planemo upload commit b'f16e028df365af5bc6b4b441152d278a55e40ffe\n'-dirty
author jpayne
date Wed, 06 Dec 2017 14:45:13 -0500
parents 628a56494663
children 881a24a35480
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2:628a56494663 3:b7bbe08d50df
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="binary" version="1.5">samtools</requirement> 4 <requirement type="Tool_Shed_Package" version="1.5">samtools</requirement>
5 <requirement type="binary" version="2.26">bedtools</requirement> 5 <requirement type="Tool_Shed_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
10 -fq2 $mapped_2 && echo "mapped out" && 10 -fq2 $mapped_2 && echo "mapped out" &&