|
7
|
1 <tool id="varscan" name="VarScan Readcount" version="2.0">
|
|
5
|
2 <description>To use varscan readcount tool</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="2.4.4">varscan</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command detect_errors="exit_code"><![CDATA[
|
|
9
|
7 varscan readcounts '${input}' --min-coverage '${min_cov}' --output-file '${output}'
|
|
5
|
8 ]]></command>
|
|
|
9 <inputs>
|
|
|
10 <param name="input" format="pileup" type="data" label="Pileup dataset"/>
|
|
9
|
11 <param name="min_cov" type="integer" value="1" min="1" max="2000" label="Minimum read depth" help="Minimum depth at a position to make a call (default: 1)"/>
|
|
5
|
12 </inputs>
|
|
|
13 <outputs>
|
|
|
14 <data name="output" format="vcf"/>
|
|
|
15 </outputs>
|
|
8
|
16 <help>
|
|
|
17 USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS
|
|
|
18 OPTIONS:
|
|
|
19 --output-file Output file to contain the readcounts
|
|
|
20 --min-coverage Minimum read depth at a position to make a call (default: 1)
|
|
|
21 --min-base-qual Minimum base quality at a position to count a read (default: 20)
|
|
|
22 </help>
|
|
0
|
23 </tool>
|
