diff cuffdiff_wrapper.xml @ 14:d10befb0867a

Add library_norm_method and dispersion_method params to cuffdiff tool.

--- 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."/>