1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9aec3401a724/ changeset: 9aec3401a724 user: jgoecks date: 2012-12-04 03:02:45 summary: Enable and document GFF annotation support for Cuffcompare/merge/diff. affected #: 3 files
diff -r 1ac27213bafb6d3fef210c17728eeef0338bd8ad -r 9aec3401a724eeb8e47a13de6de13c1eb122026c tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml +++ b/tools/ngs_rna/cuffcompare_wrapper.xml @@ -48,7 +48,7 @@ <option value="Yes">Yes</option></param><when value="Yes"> - <param format="gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/><param name="ignore_nonoverlapping_reference" type="boolean" label="Ignore reference transcripts that are not overlapped by any transcript in input files"/></when><when value="No">
diff -r 1ac27213bafb6d3fef210c17728eeef0338bd8ad -r 9aec3401a724eeb8e47a13de6de13c1eb122026c tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -72,7 +72,7 @@
</command><inputs> - <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/> + <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3/GTF file produced by cufflinks, cuffcompare, or other source."/><conditional name="group_analysis"><param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group."><option value="No">No</option>
diff -r 1ac27213bafb6d3fef210c17728eeef0338bd8ad -r 9aec3401a724eeb8e47a13de6de13c1eb122026c tools/ngs_rna/cuffmerge_wrapper.xml --- a/tools/ngs_rna/cuffmerge_wrapper.xml +++ b/tools/ngs_rna/cuffmerge_wrapper.xml @@ -47,7 +47,7 @@ <option value="Yes">Yes</option></param><when value="Yes"> - <param format="gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/></when><when value="No"></when>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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