Mercurial > repos > p.lucas > varscan_readcount
changeset 0:ef96ef60f4be draft default tip
Uploaded wrapper
| author | p.lucas |
|---|---|
| date | Tue, 13 Feb 2024 14:31:30 +0000 |
| parents | |
| children | |
| files | varscan_readcount.xml |
| diffstat | 1 files changed, 29 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/varscan_readcount.xml Tue Feb 13 14:31:30 2024 +0000 @@ -0,0 +1,29 @@ +<tool id="varscan" name="VarScan Readcount" version="3"> + <description>To use varscan readcount tool</description> + <requirements> + <requirement type="package" version="2.4.4">varscan</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + varscan readcounts '${input}' --min-coverage '${min_cov}' --min-base-qual ${min_base_qual} --output-file '${output}' + ]]></command> + <inputs> + <param name="input" format="pileup" type="data" label="Pileup dataset"/> + <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)"/> + <param name="min_base_qual" type="integer" value="20" min="1" max="500" label="Minimum base quality" help="Minimum base quality at a position to count a read (default: 20)"/> + </inputs> + <outputs> + <data name="output" format="vcf"/> + </outputs> + <help> + USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS + + OPTIONS: + + --output-file Output file to contain the readcounts + + --min-coverage Minimum read depth at a position to make a call (default: 1) + + --min-base-qual Minimum base quality at a position to count a read (default: 20) + + </help> +</tool>