Mercurial > repos > nick > allele_counts_1
changeset 15:2aa561f29da4
allele-counts.xml: Pull in new changes.
| author | nicksto <nmapsy@gmail.com> |
|---|---|
| date | Wed, 09 Dec 2015 11:13:51 -0500 |
| parents | e5d39283fe4d |
| children | 25e8f4cf2a81 |
| files | allele-counts.xml |
| diffstat | 1 files changed, 14 insertions(+), 3 deletions(-) [+] |
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--- a/allele-counts.xml Wed Dec 09 11:03:33 2015 -0500 +++ b/allele-counts.xml Wed Dec 09 11:13:51 2015 -0500 @@ -1,13 +1,14 @@ <tool id="allele_counts_1" version="1.2" name="Variant Annotator"> <description> process variant counts</description> - <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt</command> + <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt -r $seed</command> <inputs> <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/> - <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold (in percent)"/> - <param name="covg" type="integer" value="10" min="0" label="Coverage threshold (in reads per strand)"/> + <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold" help="in percent"/> + <param name="covg" type="integer" value="10" min="0" label="Coverage threshold" help="in reads (per strand)"/> <param name="nofilt" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Do not filter sites or alleles" /> <param name="stranded" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output stranded base counts" /> <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="True" label="Write header line" /> + <param name="seed" type="text" value="" label="PRNG seed" /> </inputs> <outputs> <data name="output" format="tabular"/> @@ -17,6 +18,16 @@ <exit_code range=":-1" err_level="fatal"/> </stdio> + <tests> + <test> + <param name="input" value="tests/artificial.vcf.in" /> + <param name="freq" value="10" /> + <param name="covg" value="10" /> + <param name="seed" value="1" /> + <output name="output" file="tests/artificial.csv.out" /> + </test> + </tests> + <help> .. class:: infomark