1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/237209336f03/ Changeset: 237209336f03 User: jgoecks Date: 2013-05-19 17:59:50 Summary: Add library normalization and dispersion options to Cuffdiff wrapper. Affected #: 2 files
diff -r 0afdd38eb5ec63708a58b2e2bb8aadecf7f42f72 -r 237209336f0337ea9f47df39548df3c11900f182 tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py +++ b/tools/ngs_rna/cuffdiff_wrapper.py @@ -62,6 +62,8 @@ parser.add_option( '-c', '--min-alignment-count', dest='min_alignment_count', help='The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).' ) parser.add_option( '--FDR', dest='FDR', help='The allowed false discovery rate. The default is 0.05.' ) parser.add_option( '-u', '--multi-read-correct', dest='multi_read_correct', action="store_true", help='Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome') + parser.add_option( '--library-norm-method', dest='library_norm_method' ) + parser.add_option( '--dispersion-method', dest='dispersion_method' )
# Advanced Options: parser.add_option( '--num-importance-samples', dest='num_importance_samples', help='Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000' ) @@ -143,6 +145,10 @@ cmd = "cuffdiff --no-update-check -q"
# Add options. + if options.library_norm_method: + cmd += ( " --library-norm-method %s" % options.library_norm_method ) + if options.dispersion_method: + cmd += ( " --dispersion-method %s" % options.dispersion_method ) if options.inner_dist_std_dev: cmd += ( " -s %i" % int ( options.inner_dist_std_dev ) ) if options.num_threads:
diff -r 0afdd38eb5ec63708a58b2e2bb8aadecf7f42f72 -r 237209336f0337ea9f47df39548df3c11900f182 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -9,6 +9,8 @@ --FDR=$fdr --num-threads="4" --min-alignment-count=$min_alignment_count + --library-norm-method=$library_norm_method + --dispersion-method=$dispersion_method
--isoforms_fpkm_tracking_output=$isoforms_fpkm_tracking --genes_fpkm_tracking_output=$genes_fpkm_tracking @@ -92,6 +94,18 @@ </when></conditional>
+ <param name="library_norm_method" type="select" label="Library normalization method"> + <option value="geometric" selected="True">geometric</option> + <option value="classic-fpkm">classic-fpkm</option> + <option value="quartile">quartile</option> + </param> + + <param name="dispersion_method" type="select" label="Dispersion estimation method" help="If using only one sample per condition, you must use 'blind.'"> + <option value="pooled" selected="True">pooled</option> + <option value="per-condition">per-condition</option> + <option value="blind">blind</option> + </param> + <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/><param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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