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vcftools.xml |
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| diff -r 90fe42320bd1 -r 2e09b3f332f8 vcftools.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vcftools.xml Wed Jul 10 17:23:45 2013 -0400 |
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| @@ -0,0 +1,90 @@ +<toold id="vcftools" name="VCFtools" version="0.0.1"> + <description> + The vcftools program is intended for analysis of diploid SNP data in VCF format. + </description> + <requirements> + <requirement type="package" version="0.1.11">vcftools</requirement> + </requirements> + <command> + vcftools + + #if str($basic) == "gzvcf" + --gzvcf + #elif str($basic) == "bcf" + --bcf + #else + --vcf + #end if + + $input + + #for $chromosome in $chr + --chr $chromosome.number + #end for + + #for $chromosome in $notchr + --notchr $chromosome.number + #end for + + #if str($frombp) != "" + --from-bp $frombp + #end if + + #if str($tobp) != "" + --to-bp $tobp + #end if + + #for $snp in $snps + --snp $snp.id + #end for + + #if str(${snpfile.file_name}) != "" + --snps $snpfile + #end if + + #if str(${excludesnpfile.file_name}) != "" + --snps $excludesnpfile + #end if + + #if str($indels) == "keeponlyindels" + --keep-only-indels + #elif str($indels) == "removeindels" + --removeindels + #end if + + $removefilterall $recodetostream > out.recode.vcf + </command> + <inputs> + <param name="input" type="data" label="Input vcf file" format="vcf" /> + <param name="basic" type="select" label="Basic Options" value="vcf"> + <option value="vcf">Decompressed vcf file (default)</option> + <option value="gzvcf">Compressed (gzipped) vcf file</option> + <option value="bcf">Compressed (bgzf) bcf file</option + </param> + <repeat name="chr" title="Include chromosomes to be processed"> + <param name="number" label="Chromosome number" type="integer" optional="true" /> + </repeat> + <repeat name="notchr" title="Exclude chromosomes from processing"> + <param name="number" label="Chromosome number" type="integer" optional="true" /> + </repeat> + <param name="frombp" label="Beginning of range to be processed" help="only if chromosomes are included. You must also specify the end of range to be processed." optional="true" type="integer"/> + <param name="tobp" label="End of range to be processed" optional="true" type="integer" help="only if chromosomes are included. You must also specify the beginning of range to be processed."/> + <repeat name="snps" title="SNPs to include"> + <param name="id" label="ID of SNP" type="text" optional="true" help="e.g. a dbSNP rsID"/> + </repeat>t + <param name="snpfile" type="data" format="txt, tabular" label="List of SNPs to include" help="The file should contain a list of SNP IDs (e.g. dbSNP rsIDs), with one ID per line." optional="true"/> + <param name="excludesnpfile" type="data" label = "List of SNPs to disclude" format="txt, tabular" help="The file should contain a list of SNP IDs (e.g. dbSNP rsIDs), with one ID per line." optional="true"/> + <param name="indels" type="select" label="Indel options" value="none"> + <option value="keeponlyindels">Keep only indels</option> + <option value="removeindels"> Remove indels</option> + </param> + <param name="removefilterall" type="boolean" truevalue="--remove-filtered-all" falsevalue="" label="Remove all sites with the FILTER tag" value="false" /> + <param name="recodetostream" type="boolean" truevalue="--recode-to-stream" falsevalue="" label="Recode to stream" value="false" /> + </inputs> + <outputs> + <data format="vcf" name="output" from_work_dir="out.recode.vcf"> + </outputs> + <help> + Welcome to VCFtools - a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide methods for working with VCF files: validating, merging, comparing and calculate some basic population genetic statistics. More information at http://vcftools.sourceforge.net/index.html. + </help> + |