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comparison samblaster.xml @ 1:4f68e55100c3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 458f23548658ba4dd7960e1825cdb22c82616e7f
author mvdbeek
date Fri, 16 Dec 2016 05:44:40 -0500
parents 5743b5c0209b
children 5d1a1388a036
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0:5743b5c0209b 1:4f68e55100c3
1 <tool id="samblaster" name="samblaster" version="0.1.24"> 1 <tool id="samblaster" name="samblaster" version="0.1.24.1">
2 <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description> 2 <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.24">samblaster</requirement> 4 <requirement type="package" version="0.1.24">samblaster</requirement>
5 <requirement type="package" version="1.3.1">samtools</requirement> 5 <requirement type="package" version="1.3.1">samtools</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 samtools sort -O sam -n '$input' | 8 samtools sort -@ \$GALAXY_SLOTS:-4 -m 4G -O sam -n '$input' |
9 samblaster 9 samblaster
10 $output 10 $output
11 $discordantFile 11 $discordantFile
12 $splitterFile 12 $splitterFile
13 $unmappedFile 13 $unmappedFile
22 --minNonOverlap '$minNonOverlap' 22 --minNonOverlap '$minNonOverlap'
23 --minClipSize '$minClipSize' && sleep 1 23 --minClipSize '$minClipSize' && sleep 1
24 ]]></command> 24 ]]></command>
25 <inputs> 25 <inputs>
26 <param name="input" argument="--input" type="data" format="bam,sam"/> 26 <param name="input" argument="--input" type="data" format="bam,sam"/>
27 <param name="output" argument="--ouput" label="Output bam file for all input alignments" type="boolean" truevalue="-o >(samtools sort -O bam -o output.bam)" falsevalue="-o /dev/null"/> 27 <param name="output" argument="--ouput" label="Output bam file for all input alignments" type="boolean" truevalue="-o >(samtools sort -@ \$GALAXY_SLOTS:-4 -m 2G -O bam -o output.bam)" falsevalue="-o /dev/null"/>
28 <param name="discordantFile" argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d >(samtools sort -O bam -o discordant.bam)" falsevalue=""/> 28 <param name="discordantFile" argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d >(samtools sort -@ \$GALAXY_SLOTS:-4 -m 2G -O bam -o discordant.bam)" falsevalue=""/>
29 <param name="splitterFile" argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s >(samtools sort -O bam -o splitter.bam)" falsevalue=""/> 29 <param name="splitterFile" argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s >(samtools sort -@ \$GALAXY_SLOTS:-4 -m 2G -O bam -o splitter.bam)" falsevalue=""/>
30 <param name="unmappedFile" argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/> 30 <param name="unmappedFile" argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/>
31 <param name="acceptDupMarks" argument="--acceptDupMarks" label="Accept duplicate marks already in input file instead of looking for duplicates in the input?" type="boolean" truevalue="-a" falsevalue=""/> 31 <param name="acceptDupMarks" argument="--acceptDupMarks" label="Accept duplicate marks already in input file instead of looking for duplicates in the input?" type="boolean" truevalue="-a" falsevalue=""/>
32 <param name="excludeDups" argument="--excludeDups" label="Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file?" type="boolean" truevalue="-a" falsevalue=""/> 32 <param name="excludeDups" argument="--excludeDups" label="Exclude reads marked as duplicates from discordant, splitter, and/or unmapped file?" type="boolean" truevalue="-a" falsevalue=""/>
33 <param name="removeDups" argument="--removeDups" label="Remove duplicates reads from all output files?" help="(Implies --excludeDups)" type="boolean" truevalue="-e" falsevalue=""/> 33 <param name="removeDups" argument="--removeDups" label="Remove duplicates reads from all output files?" help="(Implies --excludeDups)" type="boolean" truevalue="-e" falsevalue=""/>
34 <param name="addMateTags" argument="--addMateTags" label="Add MC and MQ tags?" type="boolean" truevalue="--addMateTags" falsevalue=""/> 34 <param name="addMateTags" argument="--addMateTags" label="Add MC and MQ tags?" type="boolean" truevalue="--addMateTags" falsevalue=""/>