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comparison lumpy_preprocessing.xml @ 1:b24b84398cf4 draft default tip

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"planemo upload for repository https://github.com/arq5x/lumpy-sv commit 41cb10683d89fa20e122f4c60b8f5bf0e3c390d8"
author iuc
date Sat, 10 Jul 2021 07:39:27 +0000
parents 39f0493905cf
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0:39f0493905cf 1:b24b84398cf4
1 <tool id="lumpy_prep" name="LUMPY preprocessing" version="@WRAPPER_VERSION@"> 1 <tool id="lumpy_prep" name="LUMPY preprocessing" version="@WRAPPER_VERSION@" profile="20.05">
2 <description>extracts discordant read pairs and split-read alignments from a BAM dataset</description> 2 <description>extracts discordant read pairs and split-read alignments from a BAM dataset</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">lumpy-sv</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">lumpy-sv</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 set -o pipefail;
11
10 samtools collate -O --output-fmt sam '$bam_in' | samblaster $dup_handling --addMateTags | samtools view -bS - > blasted.bam && 12 samtools collate -O --output-fmt sam '$bam_in' | samblaster $dup_handling --addMateTags | samtools view -bS - > blasted.bam &&
11 13
12 samtools view -b -F 1294 blasted.bam > discordants.unsorted.bam && 14 samtools view -b -F 1294 blasted.bam > discordants.unsorted.bam &&
13 samtools view -h blasted.bam | extractSplitReads_BwaMem -i stdin | samtools view -Sb - > splitters.unsorted.bam && 15 samtools view -h blasted.bam | extractSplitReads_BwaMem -i stdin | samtools view -Sb - > splitters.unsorted.bam &&
14 16
32 </outputs> 34 </outputs>
33 <tests> 35 <tests>
34 <test> 36 <test>
35 <param name="bam_in" ftype="bam" value="sample.bam" /> 37 <param name="bam_in" ftype="bam" value="sample.bam" />
36 <param name="dup_handling" value="" /> 38 <param name="dup_handling" value="" />
37 <output name="blasted_bam" ftype="qname_sorted.bam" file="blasted.bam" /> 39 <output name="blasted_bam" ftype="qname_sorted.bam" file="blasted.bam" lines_diff="2"/>
38 <output name="discordants_bam" ftype="bam" file="discordants.bam" /> 40 <output name="discordants_bam" ftype="bam" file="discordants.bam" lines_diff="2"/>
39 <output name="splitters_bam" ftype="bam" file="splitters.bam" /> 41 <output name="splitters_bam" ftype="bam" file="splitters.bam" lines_diff="2"/>
40 </test> 42 </test>
41 </tests> 43 </tests>
42 <help><![CDATA[ 44 <help><![CDATA[
43 **What it does** 45 **What it does**
44 46