Devteam:

Btw, I found this problem also exists in the variant_filtration tool
from the main toolshed. Same situation: comment out the <filter> and
the tool detects and populates reference genomes properly.

Cheers,
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu


On Wed, Dec 3, 2014 at 8:01 AM, Evan Bollig PhD <boll0...@umn.edu> wrote:
> 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
> &amp;lt;variant&amp;gt;" />
>          <param name="ref_file" type="select" label="Using reference
> genome" help="-R,--reference_sequence
> &amp;lt;reference_sequence&amp;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
> e...@msi.umn.edu
> boll0...@umn.edu
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