Mercurial > repos > yusuf > dedup_realign_bam

comparison DedupRealignBAM.xml @ 0:6b673ffd9e38 default tip

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author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:29:45 -0600
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1 <?xml version="1.0"?>
2
3 <tool id="dedup_realign_bam_1" name="Deduplicate and realign a BAM file(s)">
4 <description>using samtools and GATK</description>
5 <version_string>echo 1.0.0</version_string>
6 <command interpreter="perl">prep_bams $__tool_data_path__ $messages $ref_genome\.fa ${__new_file_path__} $prepped_bam_file $input_bam_file
7 #for $i in $inputs
8 ${i.input}
9 #end for
10 </command>
11 <inputs>
12 <param name="ref_genome" type="genomebuild" label="Reference genome" help="against which the reads were mapped"/>
13 <param format="bam" name="input_bam_file" type="data" label="Source BAM (mapped reads) file" help="Need to merge multiple input BAM files for one sample? Use controls below."/>
14 <repeat name="inputs" title="Input BAM Files">
15 <param name="input" label="Additional BAM file to merge" type="data" format="bam" />
16 </repeat>
17
18 </inputs>
19 <outputs>
20 <data name="prepped_bam_file" format="bam" type="data" label="Deduped and realigned mapped reads"/>
21 <data name="messages" format="text" type="data" label="Prep process log messages"/>
22 </outputs>
23
24 <tests/>
25
26 <help>
27 This tool runs a set of processes to first optionally merge BAMs, then deduplicate (samtools) and realign (GATK) the reads mapped to a reference genome.
28 This is important for genotyping studies. While these steps could be run independently in a workflow,
29 an enormous amount of intermediate data files are generated. This tool cleans up those intermediate files.
30 </help>
31
32 </tool>