# HG changeset patch
# User kkonganti
# Date 1657735996 14400
# Node ID 4e72dfe54475b0345cd42347101f689e54b826fb
# Parent  905def920829251e38114009d3debf8d5b56dfd0
"planemo upload"

diff -r 905def920829 -r 4e72dfe54475 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jul 13 14:10:46 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 13 14:13:16 2022 -0400
@@ -15,10 +15,10 @@
 	    #end for
     #elif (str($input_read_type_cond.input_read_type) == "paired"):
         #for _, $pair in enumerate($input_read_type_cond.input_pair)
-            #set $read_R1 = os.path.basename(str(${pair.forward}))
-            #set $read_R2 = os.path.basename(str(${pair.reverse}))
-	        ln -sf '${pair.forward}' './cpipes-input/${read_R1.name}';
-	        ln -sf '${pair.reverse}' './cpipes-input/${read_R2.name}';
+            #set $read_R1 = os.path.basename(str($pair.forward))
+            #set $read_R2 = os.path.basename(str($pair.reverse))
+	        ln -sf '$pair.forward' './cpipes-input/${read_R1.name}';
+	        ln -sf '$pair.reverse' './cpipes-input/${read_R2.name}';
 	    #end for
     #end if
 	$__tool_directory__/0.2.1/cpipes
@@ -104,7 +104,7 @@
                             help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS."/>
                     </when>
                 </conditional>
-                <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
+                <param name="fq_suffix" value="_R1_001.fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
                 <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/>
             </when>
         </conditional>