--- a/cfsan_snp_pipeline_merge_vcfs.xml	Wed Nov 22 15:34:14 2023 +0000
+++ b/cfsan_snp_pipeline_merge_vcfs.xml	Wed Nov 22 20:59:14 2023 +0000
@@ -5,28 +5,21 @@
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-python '$__tool_directory__/snp_wind.py' ./
-#if str($input_type_cond.input_type) == 'single':
-    -n '$input_vcf.element_identifier'
-    -f '$input_vcf'
-#else:
-    #for $input_vcf in $input_vcf_collection
-        -n '$input_vcf.element_identifier'
-        -f '$input_vcf'
-    #end for
-#end if
--p 'consensus.vcf' > ./file
+python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.vcf'
+#for $input_vcf in $input_vcf_collection
+    -n '$input_vcf.element_identifier' -f '$input_vcf'
+#end for
+> ./file
 && cfsan_snp_pipeline merge_vcfs ./file
     ]]></command>
     <inputs>
-        <expand macro="input_type_cond"/>
+        <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/>
     </inputs>
     <outputs>
         <data name="output" format="vcf"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_type" value="collection"/>
             <param name="input_vcf_collection">
                 <collection type="list">
                     <element name="sample1" value="samples/sample1/consensus.vcf" ftype="vcf"/>