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comparison paired_bam_dealer.xml @ 4:881a24a35480

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planemo upload commit b'f16e028df365af5bc6b4b441152d278a55e40ffe\n'-dirty
author jpayne
date Wed, 06 Dec 2017 16:41:46 -0500
parents b7bbe08d50df
children 55df0d1c6365
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3:b7bbe08d50df 4:881a24a35480
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="Tool_Shed_Package" version="1.5">samtools</requirement> 4 <requirement type="package" version="1.5">samtools</requirement>
5 <requirement type="Tool_Shed_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 which -a samtools ; ldd `which samtools`
9 -fq $mapped_1
10 -fq2 $mapped_2 && echo "mapped out" &&
11 bamToFastq -i <(
12 samtools merge -u -
13 <(samtools view -u -f 4 -F 264 $input_bam)
14 <(samtools view -u -f 8 -F 260 $input_bam)
15 <(samtools view -u -f 12 -F 256 $input_bam)
16 | samtools sort -n
17 )
18 -fq $unmapped_1
19 -fq2 $unmapped_2 && echo "unmapped out"
20 ]]></command> 9 ]]></command>
21 <inputs> 10 <inputs>
22 <param format="bam" name="input_bam" type="data" label="BAM alignment" /> 11 <param format="bam" name="input_bam" type="data" label="BAM alignment" />
23 </inputs> 12 </inputs>
24 <outputs> 13 <outputs>