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comparison samblaster.xml @ 2:5d1a1388a036 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 74140aea5e42e1d8e1204c7f1a256761e1861c57
author mvdbeek
date Sun, 18 Dec 2016 07:54:53 -0500
parents 4f68e55100c3
children
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1:4f68e55100c3 2:5d1a1388a036
1 <tool id="samblaster" name="samblaster" version="0.1.24.1"> 1 <tool id="samblaster" name="samblaster" version="0.1.24.2">
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="0.6.5">sambamba</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 samtools sort -@ \$GALAXY_SLOTS:-4 -m 4G -O sam -n '$input' | 8 #if $input.is_of_type('sam'):
9 #set stream="<(sambamba view -S -f bam -t ${GALAXY_SLOTS:-4} -h '%s')" % $input
10 #else:
11 #set stream="'%s'" % $input
12 #end if
13 sambamba view -t \${GALAXY_SLOTS:-4} -h <(sambamba sort -t \${GALAXY_SLOTS:-4} -n $stream -o /dev/stdout) |
9 samblaster 14 samblaster
10 $output 15 $output
11 $discordantFile 16 $discordantFile
12 $splitterFile 17 $splitterFile
13 $unmappedFile 18 $unmappedFile
18 $compatibility_mode 23 $compatibility_mode
19 --maxSplitCount '$maxSplitCount' 24 --maxSplitCount '$maxSplitCount'
20 --maxUnmappedBases '$maxUnmappedBases' 25 --maxUnmappedBases '$maxUnmappedBases'
21 --minIndelSize '$minIndelSize' 26 --minIndelSize '$minIndelSize'
22 --minNonOverlap '$minNonOverlap' 27 --minNonOverlap '$minNonOverlap'
23 --minClipSize '$minClipSize' && sleep 1 28 --minClipSize '$minClipSize'
29 #if $output != "-o /dev/null":
30 && sambamba sort -o output.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam output.sam)
31 #end if
32 #if $discordantFile:
33 && sambamba sort -o discordant.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam discordant.sam)
34 #end if
35 #if $splitterFile:
36 && sambamba sort -o splitter.bam -l 6 -t \${GALAXY_SLOTS:-4} <(sambamba view -S -f bam splitter.sam)
37 #end if
24 ]]></command> 38 ]]></command>
25 <inputs> 39 <inputs>
26 <param name="input" argument="--input" type="data" format="bam,sam"/> 40 <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 -@ \$GALAXY_SLOTS:-4 -m 2G -O bam -o output.bam)" falsevalue="-o /dev/null"/> 41 <param name="output" argument="--ouput" label="Output bam file for all input alignments" type="boolean" truevalue="-o output.sam" falsevalue="-o /dev/null"/>
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=""/> 42 <param name="discordantFile" argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d discordant.sam" 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=""/> 43 <param name="splitterFile" argument="--splitterFile" label="Output split reads?" type="boolean" truevalue="-s splitter.sam" falsevalue=""/>
30 <param name="unmappedFile" argument="--unmappedFile" label="Output unmapped/clipped reads as FASTQ?" type="boolean" truevalue="-u unmapped.fastq" falsevalue=""/> 44 <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=""/> 45 <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=""/> 46 <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=""/> 47 <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=""/> 48 <param name="addMateTags" argument="--addMateTags" label="Add MC and MQ tags?" type="boolean" truevalue="--addMateTags" falsevalue=""/>
58 <param name="input" value="sr.input.bam"/> 72 <param name="input" value="sr.input.bam"/>
59 <param name="output" value="true"/> 73 <param name="output" value="true"/>
60 <param name="discordandFile" value="false"/> 74 <param name="discordandFile" value="false"/>
61 <param name="splitterFile" value="true"/> 75 <param name="splitterFile" value="true"/>
62 <param name="unmappedFile" value="true"/> 76 <param name="unmappedFile" value="true"/>
63 <output name="output_bam" file="output.bam"/> 77 <output name="output_bam" file="output.bam" lines_diff="10"/>
64 <output name="splitter_bam" file="splitters.bam"/> 78 <output name="splitter_bam" file="splitters.bam" lines_diff="10"/>
79 <output name="unmapped_fastq" file="unmapped.fastq"/>
80 </test>
81 <test>
82 <param name="input" value="sr.input.sam" ftype="sam"/>
83 <param name="output" value="true"/>
84 <param name="discordandFile" value="false"/>
85 <param name="splitterFile" value="true"/>
86 <param name="unmappedFile" value="true"/>
87 <output name="output_bam" file="output.bam" lines_diff="10"/>
88 <output name="splitter_bam" file="splitters.bam" lines_diff="10"/>
65 <output name="unmapped_fastq" file="unmapped.fastq"/> 89 <output name="unmapped_fastq" file="unmapped.fastq"/>
66 </test> 90 </test>
67 </tests> 91 </tests>
68 <help><![CDATA[ 92 <help><![CDATA[
69 93