Mercurial > repos > gregory-minevich > bcftools_view
diff bcftools_view.xml @ 8:6572c40a8505 draft default tip
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| author | gregory-minevich |
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| date | Mon, 08 Oct 2012 16:12:40 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_view.xml Mon Oct 08 16:12:40 2012 -0400 @@ -0,0 +1,163 @@ +<tool id="bcftools_view" name="bcftools view" version="0.0.1"> + <description>Converts BCF format to VCF format</description> + <requirements> + <requirements type="package">samtools</requirements> + </requirements> + <command interpreter="python"> + bcftools_view.py bcftools view + #if str( $A ) == "true": + -A + #end if + #if str( $b ) == "true": + -b + #end if + #if $D.seq_dictionary == "true": + -D "$D.input" + #end if + #if str( $F ) == "true": + -F + #end if + #if str( $G ) == "true": + -G + #end if + #if str( $N ) == "true": + -N + #end if + #if str( $S ) == "true": + -S + #end if + #if str( $u) == "true": + -u + #end if + #if str( $c ) == "true": + -c + #end if + #if str( $e ) == "true": + -e + #end if + #if str( $g ) == "true": + -g + #end if + #if $i.alt_indel_snp_ratio == "true": + -i $i.ratio + #end if + #if $p.variant_filter == "true": + -p $p.float_value + #end if + #if $t.mutation_rate == "true": + -t $t.rate + #end if + #if str( $v ) == "true": + -v + #end if + $input + > $output + </command> + <inputs> + <param name="input" type="data" format="bcf" label="Choose a bcf file to view" /> + <param name="A" type="select" label="Retain all possible alternate alleles at variant sites"> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="b" type="select" label="Output in the BCF format. The default is VCF."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <conditional name="D"> + <param name="seq_dictionary" type="select" label="Sequence dictionary (list of chromosome names) for VCF->BCF conversion."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="input" type="data" format="tabular" label="Sequence dictionary" /> + </when> + </conditional> + <param name="F" type="select" label="Indicate PL is generated by r921 or before (ordering is different)."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="G" type="select" label="Suppress all individual genotype information."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="N" type="select" label="Skip sites where the REF field is not A/C/G/T"> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="S" type="select" label="The input is VCF instead of BCF."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="u" type="select" label="Uncompressed BCF output."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="c" type="select" label="Call variants using Bayesian inference. Automatically performs max-likelihood inference only"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <param name="e" type="select" label="Perform max-likelihood inference only, including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <param name="g" type="select" label="Call per-sample genotypes at variant sites"> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + <conditional name="i"> + <param name="alt_indel_snp_ratio" type="select" label="Use alternate INDEL-to-SNP mutation rate, default 0.15."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="ratio" type="float" label="Ratio (float)" value="0.15" /> + </when> + </conditional> + <conditional name="p"> + <param name="variant_filter" type="select" > + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="float_value" type="float" label="Float" value="0.5" /> + </when> + </conditional> + <conditional name="t"> + <param name="mutation_rate" type="select" label="Specify scaled mutation rate for variant calling, default is 0.001."> + <option value="true">Yes</option> + <option value="false" selected="true">No</option> + </param> + <when value="true"> + <param name="rate" type="float" label="Mutation Rate (float)" value="0.001" /> + </when> + </conditional> + <param name="v" type="select" label="Output variant sites only."> + <option value="true" selected="true">Yes</option> + <option value="false">No</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + <help> +**What it does:** + +This tool converts BCF files into VCF files using BCFtools view from the SAMtools set of utilities: + +http://samtools.sourceforge.net/samtools.shtml#4 + +------ + +**Citation:** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + + +If you use this tool within Galaxy, please cite `Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)`__ + + .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html + +Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.) + + </help> +</tool>