|
0
|
1 <tool id="muse" name="muse_sump" version="1.0.rc">
|
|
|
2 <description>Second 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="0.2.5" >tabix</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command> <![CDATA[bgzip -c $input2 > dbsnp.vcf.gz && tabix -p vcf -f dbsnp.vcf.gz && MuSE sump -O prova $selection -I $input1 -D dbsnp.vcf.gz]]></command>
|
|
|
8 <inputs>
|
|
|
9 <param format="txt" name="input1" type="data" label="MuSE call output" help="txt file from MuSE call"/>
|
|
|
10 <param format="vcf" name="input2" type="data" label="dbSNP vcf file" help="dbSNP vcf file"/>
|
|
|
11 <param name="selection" type="select" label="List Selection">
|
|
|
12 <option value="-E" selected="true">input generated from whole exome sequencing</option>
|
|
|
13 <option value="-G" >input generated from whole genome sequencing</option>
|
|
|
14 </param>
|
|
|
15 </inputs>
|
|
|
16 <outputs>
|
|
|
17 <data format="vcf" name="output" from_work_dir="prova" label="${tool.name} on ${on_string}"/>
|
|
|
18 </outputs>
|
|
|
19 <tests>
|
|
|
20 <test>
|
|
|
21 <param name="input1" value="results.txt"/>
|
|
|
22 <param name="input2" value="dbsnp.vcf"/>
|
|
|
23 <output name="output" file="sump_results.vcf" lines_diff="10"/>
|
|
|
24 </test>
|
|
|
25 </tests>
|
|
|
26 <help>
|
|
|
27 **MuSE sump**, takes as input the output file from ‘MuSE call’ and the dbSNP file.
|
|
|
28 More information at MuSE: http://bioinformatics.mdanderson.org/main/MuSE
|
|
|
29
|
|
|
30 Galaxy wrapper for MuSE sump implements all options available through the command line.Supported options are described below.
|
|
|
31
|
|
|
32 Usage: MuSE sump [options]
|
|
|
33 Options:
|
|
|
34 -I FILE single input file generated by 'MuSE call'
|
|
|
35 -G input generated from whole genome sequencing data
|
|
|
36 -E input generated from whole exome sequencing data
|
|
|
37 -O STR output file name (VCF format)
|
|
|
38 -D FILE dbSNP vcf file that should be bgzip compressed,
|
|
|
39 tabix indexed and based on the same reference
|
|
|
40 genome used in 'MuSE call'.
|
|
|
41 **IMPORTANT** the wrapper will automatically compress the vcf and create the tabix index
|
|
|
42
|
|
|
43
|
|
|
44 </help>
|
|
|
45 <citations>
|
|
|
46 <citation type="doi">10.1186/s13059-016-1029-6</citation>
|
|
|
47 </citations>
|
|
|
48 </tool>
|
