# HG changeset patch
# User kkonganti
# Date 1657746176 14400
# Node ID 022230c283f2703e62b209b507dd824501474960
# Parent  de5b87ce9fe42fa2d92c711d88b9f5bdc68cc07d
"planemo upload"

diff -r de5b87ce9fe4 -r 022230c283f2 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jul 13 16:51:33 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 13 17:02:56 2022 -0400
@@ -10,17 +10,22 @@
     pwd_path=\$(pwd);
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
 	    #for _, $unpaired in enumerate($input_read_type_cond.input):
+            #set read1 = str($unpaired.name)
             #if not str($unpaired.name).endswith(('.fastq', '.fastq.gz')):
-                #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext)
-            #else:
-                #set read1 = str($unpaired.name)
+                #set read1 = str($unpaired.name) + str('.') + str($unpaired.ext)    
             #end if
             ln -sf '$unpaired' './cpipes-input/$read1';
 	    #end for
     #elif (str($input_read_type_cond.input_read_type) == "paired"):
 	    #for _, $pair in enumerate($input_read_type_cond.input_pair)
-	        #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext)
-	        #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext)
+            #set read_R1 = str($pair.forward.name)
+            #set read_R2 = str($pair.reverse.name)
+            #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')):
+	            #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext)
+            #end if
+            #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')):
+                #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext)
+            #end if
 	        ln -sf '$pair.forward' './cpipes-input/$read_R1';
 	        ln -sf '$pair.reverse' './cpipes-input/$read_R2';
 	    #end for
@@ -96,8 +101,7 @@
                 <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the Unpaired FASTQ"/>
             </when>
             <when value="paired">
-                <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz"
-                    label="List of Dataset pairs" />
+                <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz" label="List of Dataset pairs" />
                 <conditional name="pipeline_cond">
                     <param name="pipeline" type="select" label="CPIPES Workflow name"
                         help="Auto selected centriflaken_hy for paired-end short reads.">