| Next changeset 1:e88316dc99b5 (2014-08-14) |
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Commit message:
Imported from capsule None |
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added:
bcftools_macros.xml bcftools_view.xml tool_dependencies.xml |
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| diff -r 000000000000 -r bdd0cb7fbedf bcftools_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_macros.xml Thu Aug 14 11:46:32 2014 -0400 |
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| @@ -0,0 +1,27 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>@EXECUTABLE@ 2>&1 | head -n 3 | tail -n 1</version_command> + </xml> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <yield /> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r bdd0cb7fbedf bcftools_view.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bcftools_view.xml Thu Aug 14 11:46:32 2014 -0400 |
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| @@ -0,0 +1,94 @@ +<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> |
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| diff -r 000000000000 -r bdd0cb7fbedf tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Aug 14 11:46:32 2014 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |