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author elixir-it
date Mon, 02 Jul 2018 10:40:32 -0400
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1 <tool id="muse_call" name="muse call" version="1.0.rc">
2 <description>First step of somatic point mutation caller for tumor-normal paired samples in next-generation sequencing data.</description>
3 <requirements>
4 <requirement type="package" version="1.0.rc" >muse</requirement>
5 <requirement type="package" version="1.7">samtools</requirement>
6 </requirements>
7 <command> <![CDATA[
8 ##creation of the bam indexes and execution of the MuSE call command with all the advanced options
9 samtools index $input2 && samtools index $input3 && MuSE call -O variant_call -f $input1 $input2 $input3
10 #if $region
11 -r $region
12 #end if
13 #if $positions
14 -l $positions
15 #end if]]>
16 </command>
17 <inputs>
18 <param format="fasta" name="input1" type="data" label="reference" help="fasta"/>
19 <param format="bam" name="input2" type="data" label="tumor bam" help="tumor sample bamfile"/>
20 <param format="bam" name="input3" type="data" label="normal bam" help="normal sample bamfile"/>
21 <param name="region" type="text" optional="true" label="region" help="(chr:pos-pos)"/>
22 <param format="txt,bed" name="positions" type="data" optional="true" label="list of regions" help="file txt or BED (chr:pos-pos or BED),with one region per line" />
23 </inputs>
24 <outputs>
25 <data format="txt" name="output" from_work_dir="variant_call.MuSE.txt" label="${tool.name} on ${on_string}"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="input1" value="test_fasta.fa" ftype="fasta"/>
30 <param name="input2" value="Muse_test_tumoral.bam"/>
31 <param name="input3" value="Muse_test_normal.bam"/>
32 <output name="output" file="results.txt" lines_diff="8"/>
33 </test>
34 </tests>
35 <help>
36 **MuSE call**, takes as input the indexed reference genome FASTA file and the BAM file from normal and tumoral sample.
37 The BAM files require aligning all the sequence reads against the reference genome using the Burrows-Wheeler alignment tool (BWA),
38 with either the backtrack or the maximal exact matches (MEM) algorithm. In addition,
39 the BAM files need to be processed by following the Genome Analysis Toolkit (GATK) Best Practices that include:
40 Marking duplicates,realigning the paired tumor-normal BAMs jointly recalibrating base quality scores.
41 More information at MuSE: http://bioinformatics.mdanderson.org/main/MuSE
42
43 Galaxy wrapper for MuSE call implements all options available through the command line. Supported options are described below.
44
45 Usage: MuSE call [options] tumor.bam matched_normal.bam
46 Options:
47 -f FILE faidx indexed reference sequence file
48 -r STR single region (chr:pos-pos) where somatic
49 mutations are called
50 -l FILE list of regions (chr:pos-pos or BED), one
51 region per line
52 -O STR output file name (suffix '.MuSE.txt' is
53 automatically added)
54 </help>
55 <citations>
56 <citation type="doi">10.1186/s13059-016-1029-6</citation>
57 </citations>
58 </tool>