1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b1d3a6a907d1/ changeset: b1d3a6a907d1 user: joachimjacob date: 2013-02-12 09:55:44 summary: Fixed --no-discordant parameter in tophat2_wrapper.xml and .py. affected #: 2 files diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r b1d3a6a907d1ee4847fbcea61a162067b3be0f49 tools/ngs_rna/tophat2_wrapper.py --- a/tools/ngs_rna/tophat2_wrapper.py +++ b/tools/ngs_rna/tophat2_wrapper.py @@ -22,7 +22,7 @@ parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) parser.add_option( '', '--read-mismatches', dest='read_mismatches' ) parser.add_option( '', '--bowtie-n', action="store_true", dest='bowtie_n' ) - parser.add_option( '', '--report-discordant-pair-alignments', action="store_true", dest='report_discordant_pairs' ) + parser.add_option( '', '--no-discordant', action="store_true", dest='report_concordant_pairs_only' ) parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' ) parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' ) @@ -141,8 +141,8 @@ opts = '-p %s %s' % ( options.num_threads, space ) if options.single_paired == 'paired': opts += ' -r %s' % options.mate_inner_dist - if options.report_discordant_pairs: - opts += ' --report-discordant-pair-alignments' + if options.report_concordant_pairs_only: + opts += ' --no-discordant' # Read group options. if options.rgid: if not options.rglb or not options.rgpl or not options.rgsm: diff -r e5dcefc328bb4fadcd0097787d167c7f43db5627 -r b1d3a6a907d1ee4847fbcea61a162067b3be0f49 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -37,8 +37,8 @@ -r $singlePaired.mate_inner_distance --mate-std-dev=$singlePaired.mate_std_dev - #if str($singlePaired.report_discordant_pairs) == "Yes": - --report-discordant-pair-alignments + #if str($singlePaired.report_discordant_pairs) == "No": + --no-discordant #end if #end if @@ -138,8 +138,8 @@ <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/><!-- Discordant pairs. --><param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?"> - <option selected="true" value="No">No</option> - <option value="Yes">Yes</option> + <option value="No">No</option> + <option selected="True" value="Yes">Yes</option></param></when></conditional> 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.