| Previous changeset 1:2276ef984c62 (2013-07-10) Next changeset 3:0bef79a36ae1 (2013-07-10) |
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Commit message:
Deleted selected files |
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removed:
vcftools.xml |
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| diff -r 2276ef984c62 -r 6ee90c4560a1 vcftools.xml --- a/vcftools.xml Wed Jul 10 17:11:18 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,90 +0,0 @@ -<toold id="vcftools" name="VCFtools"> - <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> - |