Mercurial > repos > jpayne > bam_dealer

comparison paired_bam_dealer.xml @ 5:55df0d1c6365

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planemo upload commit b'5e9a6cdf7bbe14678aa83ae2304bde4b6ad2976d\n'
author jpayne
date Thu, 07 Dec 2017 12:24:22 -0500
parents 881a24a35480
children add58a8a67f0
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4:881a24a35480 5:55df0d1c6365
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.5">samtools</requirement> 4 <requirement type="package" version="1.5">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 which -a samtools ; ldd `which samtools` 8 bamToFastq -i <(samtools sort -n <(samtools view -u -f 1 -F 12 $input_bam ))
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"
9 ]]></command> 20 ]]></command>
10 <inputs> 21 <inputs>
11 <param format="bam" name="input_bam" type="data" label="BAM alignment" /> 22 <param format="bam" name="input_bam" type="data" label="BAM alignment" />
12 </inputs> 23 </inputs>
13 <outputs> 24 <outputs>