# HG changeset patch
# User kkonganti
# Date 1657734432 14400
# Node ID ccc58509834c096e11a9073ca778c002ba6d9afa
# Parent  ec3fca35a622c652640a01fc572b9c1274467017
"planemo upload"

diff -r ec3fca35a622 -r ccc58509834c cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jul 13 13:35:25 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 13 13:47:12 2022 -0400
@@ -13,7 +13,7 @@
 	    #for $key in $input_read_type_cond.input.keys()
 	        ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key';
 	    #end for
-    #else:
+    #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'])
@@ -94,6 +94,16 @@
             <when value="paired">
                 <param name="input_pair" type="data_collection" collection_type="list:paired" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger"
                     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.">
+                        <option value="centriflaken_hy" selected="true">centriflaken_hy</option>
+                    </param>
+                    <when value="centriflaken_hy">
+                        <param name="long_read_platform" value="N/A" type="text" optional="true" label="Mention long read sequencing platform and type"
+                            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="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ"/>
             </when>