details: http://www.bx.psu.edu/hg/galaxy/rev/8e81eced2601 changeset: 1483:8e81eced2601 user: Dan Blankenberg dan@bx.psu.edu date: Wed Aug 27 12:06:47 2008 -0400 description: Allow the user to optionally set a reference sequence in GMAJ.

1 file(s) affected in this change:

tools/visualization/GMAJ.xml

diffs (23 lines):

diff -r c77dea3e745a -r 8e81eced2601 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Tue Aug 26 17:07:44 2008 -0400 +++ b/tools/visualization/GMAJ.xml Wed Aug 27 12:06:47 2008 -0400 @@ -3,6 +3,7 @@ <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command> <inputs> <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/> + <param name="refseq" label="Reference Sequence" value="" type="text" help="Leave empty to allow interactive selection."/> <repeat name="annotations" title="Annotations"> <param name="species" type="select" label="Species of Annotation" multiple="False"> <options> @@ -70,7 +71,11 @@

title = "Galaxy: $maf_input.name" alignfile = input.maf +#if $refseq.value: +refseq = $refseq +#else: refseq = any +#end if tabext = .bed .gff .gtf #if $nowarn.value: nowarn = $nowarn