Ok, made a pull request (#2263) for your consideration.
Cheers, Christopher
On 1/29/19 11:52 AM, Björn Grüning wrote:
Hi,
the best way is to fix the upstream tool definition.
https://github.com/galaxyproject/tools-iuc/blob/master/tools/picard/picard_C...
A pull request would be great! Thanks, Bjoern
Am 29.01.19 um 11:21 schrieb Previti:
Dear all,
I just fixed a bug that prevented CollectRNAmetrics (a Picard-Tool, galaxy version 2.7.1) from working with GTF annotation files:
The pre-processing step that converts gtf to the genepred format needs two extra parameters (marked red):
gtfToGenePred-genePredExt -geneNameAsName2 'test.gtf' refFlat.tab.raw
The format of my GTF is:
Seqname Source Feature Start End Score Strand Frame Attributes 3R FlyBase gene 722370 722621 . - . gene_id "FBgn0085804"; gene_name "CR41571"; gene_source "FlyBase"; gene_biotype "pseudogene";
I'm assuming this is the "standard" GTF format (according to ensembl)
How's the best way to make this type of thing known...?
Cheers, Christopher
-- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician
German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661
christopher.previti@dkfz.de http://www.dkfz.de/ www.dkfz.de http://www.dkfz.de/
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