--- a/cuffmerge_wrapper.py	Mon Jan 20 11:09:02 2014 -0500
+++ b/cuffmerge_wrapper.py	Fri Dec 19 11:59:06 2014 -0500
@@ -1,7 +1,5 @@
 #!/usr/bin/env python
 
-# Supports Cuffmerge versions 1.3 and newer.
-
 import optparse, os, shutil, subprocess, sys, tempfile
 
 def stop_err( msg ):
@@ -15,13 +13,13 @@
     parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffmerge to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.')
     parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' )
     
-    
     # Wrapper / Galaxy options.
     parser.add_option( '', '--index', dest='index', help='The path of the reference genome' )
     parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
     
     # Outputs.
     parser.add_option( '', '--merged-transcripts', dest='merged_transcripts' )
+    parser.add_option( '--min-isoform-fraction', dest='min_isoform_fraction' )
     
     (options, args) = parser.parse_args()
     
@@ -68,7 +66,8 @@
         cmd += " -g %s " % options.ref_annotation
     if options.use_seq_data:
         cmd += " -s %s " % seq_path
-        
+    if options.min_isoform_fraction:
+        cmd += " --min-isoform-fraction %s " % (options.min_isoform_fraction)
     # Add input files to a file.
     inputs_file_name = tempfile.NamedTemporaryFile( dir="." ).name
     inputs_file = open( inputs_file_name, 'w' )