1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0ef81af1de09/ changeset: 0ef81af1de09 user: jgoecks date: 2011-08-11 16:14:53 summary: Add GTF-guide option to Cufflinks wrapper. Patch from Ilya Chorny. affected #: 2 files (843 bytes) --- a/tools/ngs_rna/cufflinks_wrapper.py Thu Aug 11 09:53:14 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.py Thu Aug 11 10:14:53 2011 -0400 @@ -33,6 +33,7 @@ For, example, for paired end runs with fragments selected at 300bp, \ where each end is 50bp, you should set -r to be 200. The default is 45bp.') parser.add_option( '-G', '--GTF', dest='GTF', help='Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.' ) + parser.add_option( '-g', '--GTF-guide', dest='GTFguide', help='use reference transcript annotation to guide assembly' ) # Normalization options. parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" ) @@ -104,6 +105,8 @@ cmd += ( " -m %i" % int ( options.inner_mean_dist ) ) if options.GTF: cmd += ( " -G %s" % options.GTF ) + if options.GTFguide: + cmd += ( " -g %s" % options.GTFguide ) if options.num_importance_samples: cmd += ( " --num-importance-samples %i" % int ( options.num_importance_samples ) ) if options.max_mle_iterations: --- a/tools/ngs_rna/cufflinks_wrapper.xml Thu Aug 11 09:53:14 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Thu Aug 11 10:14:53 2011 -0400 @@ -14,9 +14,12 @@ -j $pre_mrna_fraction ## Include reference annotation? - #if $reference_annotation.use_ref == "Yes": + #if $reference_annotation.use_ref == "use reference annotation": -G $reference_annotation.reference_annotation_file #end if + #if $reference_annotation.use_ref == "use reference annotation guide": + -g $reference_annotation_guide.reference_annotation_guide_file + #end if ## Set paired-end parameters? #if $singlePaired.sPaired == "Yes": @@ -53,17 +56,21 @@ <conditional name="reference_annotation"><param name="use_ref" type="select" label="Use Reference Annotation"><option value="No">No</option> - <option value="Yes">Yes</option> + <option value="Use reference annotation">Use reference annotation</option> + <option value="Use reference annotation guide">Use reference annotation as guide</option></param><when value="No"></when> - <when value="Yes"> - <param format="gff3,gtf" name="reference_annotation_file" 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="Use reference annotation"> + <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + </when> + <when value="Use reference annotation guide"> + <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Aonnotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + </when></conditional><conditional name="bias_correction"><param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> - <option value="Yes">Yes</option><option value="No">No</option> + <option value="Yes">Yes</option></param><when value="Yes"><conditional name="seq_source"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.