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comparison allele-counts.xml @ 7:a72277535a2c

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allele-counts.xml: Fix bug causing crash when no seed is given.
author nicksto <nmapsy@gmail.com>
date Wed, 09 Dec 2015 11:37:02 -0500
parents df3b28364cd2
children 6cc488e11544
comparison
equal deleted inserted replaced
6:df3b28364cd2 7:a72277535a2c
1 <tool id="allele_counts_1" version="1.2" name="Variant Annotator"> 1 <tool id="allele_counts_1" version="1.2" name="Variant Annotator">
2 <description> process variant counts</description> 2 <description> process variant counts</description>
3 <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt -r $seed</command> 3 <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt
4 #if $seed:
5 -r $seed
6 #end if
7 </command>
4 <inputs> 8 <inputs>
5 <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/> 9 <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/>
6 <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold" help="in percent"/> 10 <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold" help="in percent"/>
7 <param name="covg" type="integer" value="10" min="0" label="Coverage threshold" help="in reads (per strand)"/> 11 <param name="covg" type="integer" value="10" min="0" label="Coverage threshold" help="in reads (per strand)"/>
8 <param name="nofilt" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Do not filter sites or alleles" /> 12 <param name="nofilt" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Do not filter sites or alleles" />