|
0
|
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>
|
