Add min, max insert size parameters to bowtie2 wrapper.

tools/sr_mapping/bowtie2_wrapper.py

@@ -18,6 +18,8 @@ def __main__():
     parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' )
     parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' )
     parser.add_option( '', '--single-paired', dest='single_paired', help='' )
+    parser.add_option( '-I', '--minins', dest='min_insert' )
+    parser.add_option( '-X', '--maxins', dest='max_insert' )
     parser.add_option( '', '--settings', dest='settings', help='' )
     parser.add_option( '', '--end-to-end', dest='end_to_end', action="store_true" )
     parser.add_option( '', '--local', dest='local', action="store_true" )
@@ -73,6 +75,11 @@ def __main__():
     
     # Set up options.
     opts = '-p %s' % ( options.num_threads )
+    if options.single_paired == 'paired':
+        if options.min_insert:
+            opts += ' -I %s' % options.min_insert
+        if options.max_insert:
+            opts += ' -X %s' % options.max_insert
     if options.settings == 'preSet':
         pass
     else:

tools/sr_mapping/bowtie2_wrapper.xml

@@ -30,6 +30,8 @@
         ## Second input only if input is paired-end.
         #if $singlePaired.sPaired == "paired"
             --input2=$singlePaired.input2
+            -I $singlePaired.minInsert
+            -X $singlePaired.maxInsert
         #end if
 
         ## Set params.
@@ -56,6 +58,8 @@
                 <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                 <param format="fastqsanger" name="input2" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                 <!-- TODO: paired-end specific parameters. -->
+                <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
+                <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
             </when>
         </conditional>
         <conditional name="refGenomeSource">