Mercurial > repos > devteam > vcftools_isec

changeset 1:9e576efe7836 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcftools/vcftools_isec commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:35:37 -0500
parents 799feac145c8
children
files tool_dependencies.xml vcftools_isec.xml
diffstat 2 files changed, 9 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Sun Nov 24 11:12:03 2013 -0500
+++ b/tool_dependencies.xml	Mon Nov 09 12:35:37 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_isec.xml	Sun Nov 24 11:12:03 2013 -0500
+++ b/vcftools_isec.xml	Mon Nov 09 12:35:37 2015 -0500
@@ -1,17 +1,17 @@
-<tool id="vcftools_isec" name="Intersect" version="0.1">
+<tool id="vcftools_isec" name="Intersect" 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 ):
+        #for i, $input in enumerate( $input_files ):
             ## Sort file.
-            vcf-sort ${input.file} > ${i}.vcf.sorted ;
+            vcf-sort ${input} > ${i}.vcf.sorted ;
 
             ## Compress.
             bgzip ${i}.vcf.sorted ;
@@ -26,13 +26,11 @@
         vcf-isec -f
         #if $complement:
         -c
-        #end if 
+        #end if
         #echo ' '.join( dataset_names ) # > ${output}
     </command>
     <inputs>
-        <repeat name="inputs" title="Dataset" min="2">
-            <param name="file" label="Dataset" type="data" format="vcf"/>
-        </repeat>
+        <param name="input_files" label="Datasets" type="data" format="vcf" min="2" multiple="True"/>
         <param name="complement" type="boolean" label="Complement intersection" help="If checked, output positions present in the first file but missing from the other files"/>
     </inputs>
 
@@ -47,8 +45,8 @@
     <tests>
         <!-- Cannot specify multiple repeats in test framework right now.
         <test>
-            <param name='inputs|1' value='1.vcf' />
-            <param name='inputs|2' value='2.vcf' />
+            <param name='input_files|1' value='1.vcf' />
+            <param name='input_files|2' value='2.vcf' />
             <param name='complement' value='False' />
             <output name='output' file='out.vcf' />
         </test>