Mercurial > repos > p.lucas > varscan_readcount

comparison varscan_readcount.xml @ 7:2709a3c1548c draft

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Uploaded minimum xml
author p.lucas
date Thu, 10 Feb 2022 12:34:34 +0000
parents 9001935fe8c0
children 939dcf9b0374
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6:9001935fe8c0 7:2709a3c1548c
1 <tool id="varscan" name="VarScan Readcount" version="2"> 1 <tool id="varscan" name="VarScan Readcount" version="2.0">
2 <description>To use varscan readcount tool</description> 2 <description>To use varscan readcount tool</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.4.4">varscan</requirement> 4 <requirement type="package" version="2.4.4">varscan</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 varscan readcounts '${input}' --min-coverage '${min_cov}' --min-base-qual '${min_base_qual}' --output-file '${output}' 7 varscan readcounts '${input}' --output-file '${output}'
8 ]]></command> 8 ]]></command>
9 <inputs> 9 <inputs>
10 <param name="input" format="pileup" type="data" label="Pileup dataset"/> 10 <param name="input" format="pileup" type="data" label="Pileup dataset"/>
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)"/>
12 <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" label="Minimum base quality at a position to count a read (default: 20)"/>
13 </inputs> 11 </inputs>
14 <outputs> 12 <outputs>
15 <data name="output" format="vcf"/> 13 <data name="output" format="vcf"/>
16 </outputs> 14 </outputs>
17 <help>
18 USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS
19 OPTIONS:
20 --output-file Output file to contain the readcounts
21 --min-coverage Minimum read depth at a position to make a call (default: 1)
22 --min-base-qual Minimum base quality at a position to count a read (default: 20)
23 </help>
24 </tool> 15 </tool>