Mercurial > repos > greg > cfsan_snp_pipeline_merge_sites

changeset 3:bb483baa0e50 draft

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Uploaded
author greg
date Wed, 22 Nov 2023 19:41:49 +0000
parents b64c03573271
children 36e984464e12
files cfsan_snp_pipeline_merge_sites.xml macros.xml
diffstat 2 files changed, 4 insertions(+), 28 deletions(-) [+]
line wrap: on
line diff
--- 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">
--- a/macros.xml	Wed Nov 22 17:59:10 2023 +0000
+++ b/macros.xml	Wed Nov 22 19:41:49 2023 +0000
@@ -8,20 +8,6 @@
             <requirement type="package" version="3.6.8">python</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>