Devteam:
The "cached" reference genome option on the variant_selector tool (Main Toolshed) does not properly load reference options into the drop down. Please comment out the following line to get it to work (the same edit was already done in Unified Genotyper tool):
########### diff -r 135e8721ffc5 variant_select.xml --- a/variant_select.xml Tue Apr 01 10:49:48 2014 -0400 +++ b/variant_select.xml Wed Dec 03 13:53:46 2014 +0000 @@ -106,7 +106,7 @@ <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &lt;variant&gt;" /> <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> <options from_data_table="gatk_picard_indexes"> - <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> + <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> ###########
Can I rely on one of you folks in devteam to post a new revision of the tool? I'd rather not maintain a full fork.
Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan@msi.umn.edu boll0107@umn.edu