Mercurial > repos > p.lucas > varscan_readcount
changeset 6:9001935fe8c0 draft
Uploaded try to fix error
| author | p.lucas |
|---|---|
| date | Thu, 10 Feb 2022 09:59:34 +0000 |
| parents | 0f875edd8d91 |
| children | 2709a3c1548c |
| files | varscan_readcount.xml |
| diffstat | 1 files changed, 3 insertions(+), 5 deletions(-) [+] |
line wrap: on
line diff
--- a/varscan_readcount.xml Thu Feb 10 09:55:55 2022 +0000 +++ b/varscan_readcount.xml Thu Feb 10 09:59:34 2022 +0000 @@ -4,21 +4,19 @@ <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 ${output} + varscan readcounts '${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 [1]"/> - <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 [20]"/> + <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" label="Minimum base quality at a position to count a read (default: 20)"/> </inputs> <outputs> <data name="output" format="vcf"/> </outputs> <help> - COMMAND: varscan readcounts --help USAGE: java -jar VarScan.jar readcounts pileup_file OPTIONS OPTIONS: - --variants-file A list of variants at which to report readcounts --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)