# HG changeset patch # User iuc # Date 1522080984 14400 # Node ID d92d6f631ff5079056eb6cb8b7bc9f1a25e7079b # Parent 586f4536fc65ab48fbae0e6f1a922d08e872929f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfsort commit c2af291b241e37e0a55adbc1fc72a9fa37d93582 diff -r 586f4536fc65 -r d92d6f631ff5 vcfsort.xml --- a/vcfsort.xml Mon Oct 03 11:22:55 2016 -0400 +++ b/vcfsort.xml Mon Mar 26 12:16:24 2018 -0400 @@ -1,23 +1,24 @@ - - Sort VCF dataset by coordinate - - macros.xml - - (grep ^"#" "${input1}"; grep -v ^"#" "${input1}" | LC_ALL=C sort -k1,1 -k2,2n -V) > "${out_file1}" - - - - - - - - - - - + + Sort VCF dataset by coordinate + + macros.xml + + "${out_file1}" + ]]> + + + + + + + + + + + - - + This tool uses native UNIX sort command to order VCF dataset in coordinate order. For technically inclined the command is:: (grep ^"#" INPUT_file ; grep -v ^"#" INPUT_file | LC_ALL=C sort -k1,1 -k2,2n -V) > OUTPUT_file @@ -25,6 +26,5 @@ .. class:: infomark The same result can be achieved with the Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order). - - +