Fixed in -central changeset 05a172868303
Thanks,
J.
On Sep 18, 2012, at 4:57 PM, Jim Johnson wrote:
> The filter on the tophat2 fusions output wasn't being evaluated correctly
> when settingsType is preSet since the param dict wouldn't then have an entry
> for 'fusion_search'
>
> $ hg diff tools/ngs_rna/tophat2_wrapper.xml
> diff -r 3f12146d6d81 tools/ngs_rna/tophat2_wrapper.xml
> --- a/tools/ngs_rna/tophat2_wrapper.xml Tue Sep 18 14:10:56 2012 -0400
> +++ b/tools/ngs_rna/tophat2_wrapper.xml Tue Sep 18 15:47:47 2012 -0500
> @@ -297,7 +297,7 @@
>
> <outputs>
> <data format="tabular" name="fusions" label="${tool.name} on
> ${on_string}: fusions" from_work_dir="tophat_out/fusions.out">
> - <filter>(params['fusion_search']['do_search'] == 'Yes')</filter>
> + <filter>(params['settingsType'] == 'full' and
> params['fusion_search']['do_search'] == 'Yes')</filter>
> </data>
> <data format="bed" name="insertions" label="${tool.name} on
> ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
> <actions>
>
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