1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/41b1080c48b9/ changeset: 41b1080c48b9 user: dan date: 2012-02-29 15:36:03 summary: Headers, which are important, are kept. Original ordering, which may be specifically needed by tools or external display applications is also maintained. affected #: 2 files

diff -r c754d8c07440e4376853eb3b804af366b1442ff0 -r 41b1080c48b9bf7e8cf70aea97987f7f026e911a lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py --- /dev/null +++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py @@ -0,0 +1,24 @@ +#!/usr/bin/env python + +""" +Uses pysam to bgzip a vcf file as-is. +Headers, which are important, are kept. +Original ordering, which may be specifically needed by tools or external display applications, is also maintained. + +usage: %prog in_file out_file +""" + +from galaxy import eggs +import pkg_resources; pkg_resources.require( "pysam" ) +import ctabix, optparse + +def main(): + # Read options, args. + parser = optparse.OptionParser() + (options, args) = parser.parse_args() + input_fname, output_fname = args + + ctabix.tabix_compress(input_fname, output_fname, force=True) + +if __name__ == "__main__": + main()

diff -r c754d8c07440e4376853eb3b804af366b1442ff0 -r 41b1080c48b9bf7e8cf70aea97987f7f026e911a lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml --- a/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml +++ b/lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip_converter.xml @@ -1,6 +1,6 @@ -<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.0" hidden="true"> +<tool id="CONVERTER_vcf_to_vcf_bgzip_0" name="Convert VCF to VCF_BGZIP" version="1.0.1" hidden="true"><!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> --> - <command interpreter="python">bgzip.py -P vcf $input1 $output1</command> + <command interpreter="python">vcf_to_vcf_bgzip.py '$input1' '$output1'</command><inputs><page><param format="vcf" name="input1" type="data" label="Choose Vcf file"/>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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