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comparison samblaster.xml @ 0:5743b5c0209b 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 04:45:26 -0500
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children 4f68e55100c3
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-1:000000000000 0:5743b5c0209b
1 <tool id="samblaster" name="samblaster" version="0.1.24">
2 <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description>
3 <requirements>
4 <requirement type="package" version="0.1.24">samblaster</requirement>
5 <requirement type="package" version="1.3.1">samtools</requirement>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 samtools sort -O sam -n '$input' |
9 samblaster
10 $output
11 $discordantFile
12 $splitterFile
13 $unmappedFile
14 $acceptDupMarks
15 $excludeDups
16 $removeDups
17 $addMateTags
18 $compatibility_mode
19 --maxSplitCount '$maxSplitCount'
20 --maxUnmappedBases '$maxUnmappedBases'
21 --minIndelSize '$minIndelSize'
22 --minNonOverlap '$minNonOverlap'
23 --minClipSize '$minClipSize' && sleep 1
24 ]]></command>
25 <inputs>
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"/>
28 <param name="discordantFile" argument="--discordantFile" label="Output discordant read pairs?" type="boolean" truevalue="-d >(samtools sort -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=""/>
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=""/>
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=""/>
34 <param name="addMateTags" argument="--addMateTags" label="Add MC and MQ tags?" type="boolean" truevalue="--addMateTags" falsevalue=""/>
35 <param name="compatibility_mode" argument="-M" label="Run in compatibility mode?" help="Both 0x100 and 0x800 are considered chimeric. Similar to BWA MEM -M option." type="boolean" truevalue="-M" falsevalue="" />
36 <param name="maxSplitCount" argument="--maxSplitCount" label="Maximum number of split alignments for a read to be included in splitter file." type="integer" value="2"/>
37 <param name="maxUnmappedBases" argument="--maxUnmappedBases" label="Maximum number of un-aligned bases between two alignments to be included in splitter file." type="integer" value="50" min="1"/>
38 <param name="minIndelSize" argument="--minIndelSize" label="Minimum structural variant feature size for split alignments to be included in splitter file." type="integer" value="50" min="1"/>
39 <param name="minNonOverlap" argument="--minNonOverlap" label="Minimum non-overlaping base pairs between two alignments for a read to be included in splitter file." type="integer" value="20" min="1"/>
40 <param name="minClipSize" argument="--minClipSize" label="Minumum number of bases a mapped read must be clipped to be included in unmapped file." type="integer" value="20" min="1"/>
41 </inputs>
42 <outputs>
43 <data name="output_bam" format="bam" label="samblaster alignments on ${on_string}" from_work_dir="output.bam">
44 <filter>output</filter>
45 </data>
46 <data name="discordant_bam" format="bam" label="samblaster discordant alignments on ${on_string}" from_work_dir="discordant.bam">
47 <filter>discordantFile</filter>
48 </data>
49 <data name="splitter_bam" format="bam" label="samblaster split alignments on ${on_string}" from_work_dir="splitter.bam">
50 <filter>splitterFile</filter>
51 </data>
52 <data name="unmapped_fastq" format="fastqsanger" label="samblaster unmapped fastq on ${on_string}" from_work_dir="unmapped.fastq">
53 <filter>unmappedFile</filter>
54 </data>
55 </outputs>
56 <tests>
57 <test>
58 <param name="input" value="sr.input.bam"/>
59 <param name="output" value="true"/>
60 <param name="discordandFile" value="false"/>
61 <param name="splitterFile" value="true"/>
62 <param name="unmappedFile" value="true"/>
63 <output name="output_bam" file="output.bam"/>
64 <output name="splitter_bam" file="splitters.bam"/>
65 <output name="unmapped_fastq" file="unmapped.fastq"/>
66 </test>
67 </tests>
68 <help><![CDATA[
69
70 ]]></help>
71 <citations>
72 <citation type="doi">10.1093/bioinformatics/btu314</citation>
73 </citations>
74 </tool>