# HG changeset patch
# User kkonganti
# Date 1657743836 14400
# Node ID eeddd4dfd7f59ff0f65cc1ad5bbf60af2f1bff49
# Parent  270e8f69228bdb4f92cb12a459bf0573c29969ea
"planemo upload"

diff -r 270e8f69228b -r eeddd4dfd7f5 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jul 13 14:45:49 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 13 16:23:56 2022 -0400
@@ -9,15 +9,20 @@
 	mkdir -p cpipes-input || exit 1;
     pwd_path=\$(pwd);
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
-	    #for $key in $input_read_type_cond.input.keys()
-	        ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key';
+	    #for _, $unpaired in enumerate($input_read_type_cond.input):
+            #if not $unpaired.ext.endswith(('.fastq', '.fastq.gz')):
+                #set read_R1 = str($unpaired.name) + str($unpaired.ext)
+            #else:
+                #set read_R1 = str($unpaired.name)
+            #end if
+            ln -sf '$unpaired' './cpipes-input/$read_R1';
 	    #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_name = str($pair.forward.name)
-            #set read_R2_name = str($pair.reverse.name)
-	        ln -sf '$pair.forward' './cpipes-input/$read_R1_name';
-	        ln -sf '$pair.reverse' './cpipes-input/$read_R2_name';
+	    #for _, $pair in enumerate($input_read_type_cond.input_pair)
+	        #set read_R1 = str($pair.forward.name) + str($pair.forward.ext)
+	        #set read_R2 = str($pair.reverse.name) + str($pair.reverse.ext)
+	        ln -sf '$pair.forward' './cpipes-input/$read_R1';
+	        ln -sf '$pair.reverse' './cpipes-input/$read_R2';
 	    #end for
     #end if
 	$__tool_directory__/0.2.1/cpipes
@@ -65,7 +70,7 @@
                 <option value="paired">Paired-End reads</option>
             </param>
             <when value="single_long">
-                <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger"
+                <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz"
                     label="Dataset list of unpaired short reads or long reads" />
                 <conditional name="pipeline_cond">
                     <param name="pipeline" type="select" label="CPIPES Workflow name"
@@ -91,7 +96,7 @@
                 <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,fastqsanger.gz,fastqsanger"
+                <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"