Hi Ilya,
You can validate dbkeys using validators including metadata,
dataset_metadata_in_file/data_table, unspecified_build and others.
Could you clarify what GATK tools you are trying to modify and exactly what you
are trying accomplish? A complete example xml file, and any additional files
(e.g. *.loc) would need to be provided to give you direction.
Thanks for using Galaxy,
Dan
On Oct 27, 2011, at 1:03 PM, Chorny, Ilya wrote:
> Hi Dan,
>
> I want to modify the wrappers to get genome information from the bam/sam
> attribute. I did this for the tophat/cufflinks wrappers. I add another option
> to select genome called attribute and then I pass $bam.metadata.dkey in the
> command line (see example below). Is this something you might be interested
> in? Can you suggest an alternative way to do this? My only concern is my
> inability to validate that the $input.metadata.dbkey exists.
>
> Thanks,
>
> Ilya
>
> See example below.
>
> #if $reference_annotation.use_ref == "Use reference annotation":
> #if
> $reference_annotation.annotationSource.reference_annotation_file == "indexed":
> -G "${ filter( lambda x: str( x[0] ) == str(
> $reference_annotation.annotationSource.indices ), $__app__.tool_data_tables[
> 'gtf_index' ].get_fields() )[0][-1] }"
> #else:
> #if
> $reference_annotation.annotationSource.reference_annotation_file ==
> "attribute":
> -G "${ filter( lambda x: str( x[0] ) == str(
> $input.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index'
> ].get_fields() )[0][-1] }"
> #else:
> -G "${reference_annotation.annotationSource.ownFile}"
> #end if
> #end if
> #end if
>
> <conditional name="annotationSource">
> <param name="reference_annotation_file" type="select"
> label="Please select a reference Aonnotation">
> <option value="indexed">Use a built-in
> index</option>
> <option value="history">Use one from the
> history</option>
> <option value="attribute">Use input bam
> metadata.dbkey attribute</option>
> </param>
> <when value="indexed">
> <param name="indices" type="select" label="Select
> genome for gtf annotation">
> <options from_data_table="gtf_index">
> <filter type="sort_by" column="3" />
> <validator type="no_options" message="No
> indexes are available for the selected input dataset" />
> </options>
> </param>
> </when>
> <when value="history">
> <param name="ownFile" type="data" format="gff3,
> gtf" label="Select a reference annotation file" />
> </when>
> </conditional>
>
>
>
> Ilya Chorny Ph.D.
> Bioinformatics Scientist I
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Work: 858.202.4582
> Email: icho...@illumina.com
> Website: www.illumina.com
>
>
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