# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1374067552 18000
# Node ID d10befb0867aa94a81dafce4a45792883f5ec697
# Parent  4597c429b6fb6f9dbb0dedc00b7ab06d345249b4
Add library_norm_method and dispersion_method params to cuffdiff tool.

diff -r 4597c429b6fb -r d10befb0867a cuffdiff_wrapper.py
--- a/cuffdiff_wrapper.py	Wed Jul 17 07:58:39 2013 -0500
+++ b/cuffdiff_wrapper.py	Wed Jul 17 08:25:52 2013 -0500
@@ -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' )
@@ -137,7 +139,6 @@
     if not os.path.exists( cuffdatadir ):
         os.makedirs( cuffdatadir )
     
-    
     # If doing bias correction, set/link to sequence file.
     if options.do_bias_correction:
         if options.ref_file != 'None':
@@ -162,6 +163,10 @@
     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:
@@ -188,7 +193,7 @@
     if options.groups:
         cmd += " --labels "
         for label in options.labels:
-            cmd += label + ","
+            cmd += '"%s",' % label
         cmd = cmd[:-1]
 
         cmd += " " + options.inputA + " "
diff -r 4597c429b6fb -r d10befb0867a cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml	Wed Jul 17 07:58:39 2013 -0500
+++ b/cuffdiff_wrapper.xml	Wed Jul 17 08:25:52 2013 -0500
@@ -10,6 +10,8 @@
             --FDR=$fdr
             --num-threads="4"
             --min-alignment-count=$min_alignment_count
+            --library-norm-method=$library_norm_method
+            --dispersion-method=$dispersion_method
 
             #if 'cuffdata' in $sel_outputs or not $output_sel:
                 --cuffdatadir=$cuffdata.extra_files_path
@@ -134,6 +136,18 @@
             </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."/>