# HG changeset patch
# User trinity_ctat
# Date 1506699483 14400
# Node ID e673d9dd4928e786654d50f4ec95e420e8d03b32
# Parent  27fe7db7444b608fd9406eef05172597836ff6cd
Changing input format type.

diff -r 27fe7db7444b -r e673d9dd4928 abundance_estimation_to_matrix.xml
--- a/abundance_estimation_to_matrix.xml	Fri Sep 29 11:26:53 2017 -0400
+++ b/abundance_estimation_to_matrix.xml	Fri Sep 29 11:38:03 2017 -0400
@@ -5,25 +5,26 @@
         <requirement type="package" version="2.7">python</requirement>
         <requirement type="package">trinity</requirement>
     </requirements>
-    <command interpreter="python">
-
-        abundance_estimation_to_matrix_wrapper.py 
+    <command>
+        <![CDATA[
+        python abundance_estimation_to_matrix_wrapper.py 
 		#for $q in $RSEM_samples
 			${q.file} "${q.column_label}"
 		#end for
+        ]]>
 
     </command>
     <inputs>
 
        <repeat name="RSEM_samples" title="RSEM abundance estimates for samples">
-              <param name="file" label="Add file" type="data" format="text"/>
+              <param name="file" label="Add file" type="data" format="txt"/>
               <param name="column_label" label="column label" type="text" />
        </repeat>
 
     </inputs>
     <outputs>
-        <data format="text" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/>
-        <data format="text" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="matrix.TMM.EXPR.matrix"/>
+        <data format="txt" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="matrix.counts.matrix"/>
+        <data format="txt" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="matrix.TMM.EXPR.matrix"/>
 	</outputs>
     <tests>
 	<test>