Mercurial > repos > devteam > vcftools_merge

changeset 2:60743b92cc26 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_merge commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:35:52 -0500
parents eb02907453b4
children
files tool_dependencies.xml vcftools_merge.xml
diffstat 2 files changed, 8 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Sun Nov 24 11:42:14 2013 -0500
+++ b/tool_dependencies.xml	Mon Nov 09 12:35:52 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="vcftools" version="0.1.11">
-        <repository changeset_revision="4081df719fff" name="package_vcftools_0_1_11" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="4081df719fff" name="package_vcftools_0_1_11" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
--- a/vcftools_merge.xml	Sun Nov 24 11:42:14 2013 -0500
+++ b/vcftools_merge.xml	Mon Nov 09 12:35:52 2015 -0500
@@ -1,17 +1,17 @@
-<tool id="vcftools_merge" name="Merge" version="0.1">
+<tool id="vcftools_merge" name="Merge" version="0.1.1">
     <description>multiple VCF datasets</description>
 
     <requirements>
         <requirement type="package">tabix</requirement>
         <requirement type="package" version="0.1.11">vcftools</requirement>
     </requirements>
-    
+
     <command>
         ## Preprocessing for each dataset.
         #set dataset_names = []
-        #for i, $input in enumerate( $inputs ):
-            ## Sort file.         
-            vcf-sort ${input.file} > ${i}.vcf.sorted ;
+        #for $i, $input in enumerate( $input_files ):
+            ## Sort file.
+            vcf-sort ${input} > ${i}.vcf.sorted ;
 
             ## Compress.
             bgzip ${i}.vcf.sorted ;
@@ -25,12 +25,10 @@
         ## Merge.
         vcf-merge
         #echo ' '.join( dataset_names ) # > ${output}
-        
+
     </command>
     <inputs>
-        <repeat name="inputs" title="Datasets to Merge" min="2">
-            <param name="file" label="Dataset" type="data" format="vcf"/>
-        </repeat>
+        <param name="input_files" label="Datasets to Merge" type="data" format="vcf" min="2" multiple="True"/>
     </inputs>
 
     <outputs>