diff cfsan_snp_pipeline_merge_sites.xml @ 3:bb483baa0e50 draft

Uploaded

--- a/cfsan_snp_pipeline_merge_sites.xml	Wed Nov 22 17:59:10 2023 +0000
+++ b/cfsan_snp_pipeline_merge_sites.xml	Wed Nov 22 19:41:49 2023 +0000
@@ -6,30 +6,20 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/snp_wind.py' ./
-#if str($input_type_cond.input_type) == 'single':
-    -n '$input_type_cond.input_vcf.element_identifier'
-    -f '$input_type_cond.input_vcf'
-#else:
-    #for $input_vcf in $input_type_cond.input_vcf_collection:
-        -n '$input_vcf.element_identifier'
-        -f '$input_vcf'
-    #end for
-#end if
+#for $input_vcf in $input_vcf_collection:
+    -n '$input_vcf.element_identifier' -f '$input_vcf'
+#end for
 -p 'var.fit.vcf' > ./file
 && cfsan_snp_pipeline merge_sites -v 4 -n 'var.fit.vcf' ./file ./filtered_snps -o '$output'
     ]]></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="tabular"/>
     </outputs>
     <tests>
         <test>
-            <param name="input_vcf" value="input1.vcf"/>
-            <output name="output" value="output.tabular"/>
-        </test>
-        <test>
             <param name="input_type" value="collection"/>
             <param name="input_vcf_collection">
                 <collection type="list">