# HG changeset patch
# User kkonganti
# Date 1657734947 14400
# Node ID 04c9f550eb0852a367e2d2e8533ebc516b82a545
# Parent  ccc58509834c096e11a9073ca778c002ba6d9afa
"planemo upload"

diff -r ccc58509834c -r 04c9f550eb08 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jul 13 13:47:12 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 13 13:55:47 2022 -0400
@@ -15,10 +15,10 @@
 	    #end for
     #elif (str($input_read_type_cond.input_read_type) == "paired"):
         #for $key in $input_read_type_cond.input_pair.keys()
-            #set $read_R1 = os.path.basename($input_read_type_cond.input_pair[$key]['forward'])
-            #set $read_R2 = os.path.basename($input_read_type_cond.input_pair[$key]['reverse'])
-	        ln -sf '$input_read_type_cond.input_pair[$key]['forward']' './cpipes-input/$read_R1';
-            ln -sf '$input_read_type_cond.input_pair[$key]['reverse']' './cpipes-input/$read_R2';
+            #set $read_R1 = os.path.basename(str($input_read_type_cond.input_pair[$key]['forward']))
+            #set $read_R2 = os.path.basename(str($input_read_type_cond.input_pair[$key]['reverse']))
+	        ln -sf "$input_read_type_cond.input_pair[$key]['forward']" './cpipes-input/$read_R1';
+            ln -sf "$input_read_type_cond.input_pair[$key]['reverse']" './cpipes-input/$read_R2';
 	    #end for
     #end if
 	$__tool_directory__/0.2.1/cpipes
@@ -96,7 +96,7 @@
                     label="List of Dataset pairs" />
                 <conditional name="pipeline_cond">
                     <param name="pipeline" type="select" label="CPIPES Workflow name"
-                        help="centriflaken_hy selected for paired-end short reads.">
+                        help="Auto selected centriflaken_hy for paired-end short reads.">
                         <option value="centriflaken_hy" selected="true">centriflaken_hy</option>
                     </param>
                     <when value="centriflaken_hy">