diff cufflinks_wrapper.xml @ 12:e6ac542a288e draft default tip

Updated Test Data

--- a/cufflinks_wrapper.xml	Fri Aug 01 09:27:09 2014 -0400
+++ b/cufflinks_wrapper.xml	Sat Aug 02 10:12:58 2014 -0400
@@ -189,7 +189,7 @@
         <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/>
         <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/>
         <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/>
-	<data format="gtf" name="skipped.gtf" label="${tool.name} on ${on_string}: Skipped Transcripts" from_working_dir="genes.fpkm_tracking"/>
+	<data format="gtf" name="skipped" label="${tool.name} on ${on_string}: Skipped Transcripts" from_working_dir="skipped.gtf"/>
     </outputs>
 
     <trackster_conf>
@@ -206,16 +206,15 @@
             <param name="min_isoform_fraction" value="0.05"/>
             <param name="pre_mrna_fraction" value="0.05"/>
             <param name="use_ref" value="No"/>
-            <param name="do_normalization" value="No" />
             <param name="do_bias_correction" value="No"/>
             <param name="multiread_correct" value="No"/>
-            <param name="length_correction" value=""/>
+            <param name="length_correction" value="Cufflinks Effective Length Correction"/>
 	    <param name="use_advanced_settings" value="No" />
             <output name="genes_expression" format="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/>
             <output name="transcripts_expression" format="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/>
             <output name="assembled_isoforms" file="cufflinks_out1.gtf"/>
             <output name="global_model" file="cufflinks_out4.txt"/>
-	   
+	    <output name="skipped" file="cufflinks_out4.gtf"/> 
         </test>
     </tests>