1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/60fee5ee38fa/ changeset: 60fee5ee38fa user: jgoecks date: 2012-10-22 16:52:48 summary: Enable Tophat, Tophat2, and Cuffdiff to accept gene annotations in GFF3 format. Thanks to Jim Johnson. affected #: 3 files

diff -r 1dc4dd32eaf8b38da3e66bdc2de287f907b3605e -r 60fee5ee38fada926d010971e49623367b78362e 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" 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 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 1dc4dd32eaf8b38da3e66bdc2de287f907b3605e -r 60fee5ee38fada926d010971e49623367b78362e tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -210,7 +210,7 @@ </param><when value="No" /><when value="Yes"> - <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> + <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/></when></conditional><conditional name="raw_juncs">

diff -r 1dc4dd32eaf8b38da3e66bdc2de287f907b3605e -r 60fee5ee38fada926d010971e49623367b78362e tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -224,7 +224,7 @@ </param><when value="No" /><when value="Yes"> - <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> + <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/></when></conditional><conditional name="raw_juncs">

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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