Mercurial > repos > iuc > bcftools
view bcftools_view.xml @ 0:bdd0cb7fbedf draft
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author | iuc |
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date | Thu, 14 Aug 2014 11:46:32 -0400 |
parents | |
children | e88316dc99b5 |
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<tool id="bcfview" name="bcftoolsView" version="0.1.19"> <description>Convert, filter, subset VCF/BCF files</description> <expand macro="requirements" /> <expand macro="version_command" /> <expand macro="stdio" /> <macros> <token name="@EXECUTABLE@">bcftools</token> <import>bcftools_macros.xml</import> </macros> <command> @EXECUTABLE@ view $A $varsitesonly $snpcalling ##$F $G $N $e $g #if str( $output_format ) == "bcf": -b #end if -D $seq_dict -i $ratio -t $rate $input > $output </command> <inputs> <param name="input" type="data" format="bcf,vcf" label="Choose a bcf file to view" /> <param name="output_format" type="select" label="Choose the output format" help="-b"> <option value="vcf" selected="true">VCF</option> <option value="bcf">BCF</option> </param> <param name="seq_dict" type="data" format="tabular" optional="True" label="List of chromosome names for conversion" help="(-D)" /> <param name="ratio" type="float" label="Use alternate INDEL-to-SNP mutation rate" value="-1" help="defaults to 0.15 (-i)" /> <param name="rate" type="float" label="Mutation rate for variant calling" value="0.001" help="default to 0.001 (-t)" /> <param name="A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Retain all possible alternate alleles at variant sites" help="-A" /> <param name="varsitesonly" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Output Potential Variant Sites Only" help="-v"/> <param name="snpcalling" type="boolean" truevalue="-c" falsevalue="" checked="false" label="SNP calling" help="Forces -e the max-likelihood inference parameter. (-c)"/> <!--param name="F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Indicate PL is generated by r921 or before (ordering is different)" help="-F" /--> <param name="G" type="boolean" truevalue="-G" falsevalue="" checked="False" label="Suppress all individual genotype information" help="-G" /> <param name="N" type="boolean" truevalue="-N" falsevalue="" checked="False" label="Skip sites where the REF field is not A/C/G/T" help="-N" /> <param name="e" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Perform max-likelihood inference only" help="Including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT. (-e)" /> <param name="g" type="boolean" truevalue="-g" falsevalue="" checked="True" label="Call per-sample genotypes at variant sites" help="-g" /> </inputs> <outputs> <data format="bcf" name="output"> <change_format> <when input="output_format" value="vcf" format="vcf" /> </change_format> </data> </outputs> <tests> </tests> <help> <![CDATA[ **BCFTools View** VCF/BCF conversion, view, subset and filter VCF/BCF files. **Input format** `BCF files <http://www.1000genomes.org/wiki/analysis/variant-call-format/bcf-binary-vcf-version-2/>`_ ------ **Outputs** VCF or BCF files ]]> </help> <expand macro="citations"/> </tool>