|
0
|
1 <tool id="ensemble_vcf" name="ensemble_vcf" version="0.1.1">
|
|
|
2
|
|
|
3 <description>
|
|
|
4 integrates VCF files from different SNV detection methods for ensemble calling.
|
|
|
5 </description>
|
|
|
6
|
|
|
7 <requirements>
|
|
4
|
8 <requirement type="package" version="0.1.2">morinkit</requirement>
|
|
0
|
9 </requirements>
|
|
|
10
|
|
|
11 <command detect_errors="aggressive">
|
|
|
12 <![CDATA[
|
|
|
13
|
|
|
14 morinkit ensemble_vcf
|
|
|
15
|
|
|
16 --output $output_vcf
|
|
|
17
|
|
|
18 --min_support $min_support
|
|
|
19
|
|
|
20 #if $sorted:
|
|
|
21 --sorted
|
|
|
22 #end if
|
|
|
23
|
|
|
24 ${" ".join(map(str, $input_vcfs))}
|
|
|
25
|
|
|
26 ]]>
|
|
|
27 </command>
|
|
|
28
|
|
|
29 <inputs>
|
|
|
30 <param name="input_vcfs" type="data" format="vcf" multiple="true" label="Input VCF Files"/>
|
|
|
31 <param name="min_support" size="4" type="float" value="0.5" label="Minimum number of supporting methods.
|
|
|
32 If less than 1, considered as minimum fraction of methods." />
|
|
|
33 <param name="sorted" type="boolean" label="Are the input VCF files sorted?" />
|
|
|
34 </inputs>
|
|
|
35
|
|
|
36 <outputs>
|
|
|
37 <data name="output_vcf" format="vcf" label="Ensemble VCF File" />
|
|
|
38 </outputs>
|
|
|
39
|
|
|
40 <help>
|
|
|
41 This tool integrates the VCF files generated by different SNV detection methods
|
|
|
42 in order to perform ensemble SNV calling.
|
|
|
43 </help>
|
|
|
44
|
|
|
45 </tool>
|
