Merged heads.

tools/ngs_rna/tophat2_wrapper.py

@@ -22,7 +22,7 @@ def __main__():
     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 @@ def __main__():
     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:

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>