Mercurial > repos > greg > cfsan_snp_pipeline_merge_vcfs

changeset 1:ab24883161d3 draft

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Uploaded
author greg
date Wed, 22 Nov 2023 20:59:14 +0000
parents e958c5f7c9d1
children 5c341fcd18ff
files cfsan_snp_pipeline_merge_vcfs.xml macros.xml
diffstat 2 files changed, 6 insertions(+), 27 deletions(-) [+]
line wrap: on
line diff
--- 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"/>
--- a/macros.xml	Wed Nov 22 15:34:14 2023 +0000
+++ b/macros.xml	Wed Nov 22 20:59:14 2023 +0000
@@ -10,20 +10,6 @@
             <requirement type="package" version="1.11">tabix</requirement>
         </requirements>
     </xml>
-    <xml name="input_type_cond">
-        <conditional name="input_type_cond">
-            <param name="input_type" type="select" label="Choose the category for the files to be analyzed">
-                <option value="single" selected="true">Single files</option>
-                <option value="collection">Collection of files</option>
-            </param>
-            <when value="single">
-                <param name="input_vcf" type="data" format="vcf" label="VCF file"/>
-            </when>
-            <when value="collection">
-                <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/>
-            </when>
-        </conditional>
-    </xml>
     <xml name="citations">
         <citations>
             <citation type="doi">10.7717/peerj-cs.20</citation>