# HG changeset patch
# User jjohnson
# Date 1483742424 18000
# Node ID bfc8ceb44c5f03fe94f84d587a03eae4813fd07a
# Parent  bf2687e2511ee9d7ad76775cde4513fad7735889
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/ensembl_variant_report commit 239c1ee096e5fc3e2e929f7bf2d4afba5c677d4b-dirty

diff -r bf2687e2511e -r bfc8ceb44c5f ensembl_variant_report.xml
--- a/ensembl_variant_report.xml	Fri Jan 06 16:28:35 2017 -0500
+++ b/ensembl_variant_report.xml	Fri Jan 06 17:40:24 2017 -0500
@@ -2,6 +2,7 @@
     <requirements>
         <requirement type="package" version="1.40">gtf_to_genes</requirement>
         <requirement type="package" version="3.1.4">twobitreader</requirement>
+        <requirement type="package" version="1.62">biopython</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -62,8 +63,8 @@
                 <param name="dpr_column" type="data_column" data_ref="input_tsv" label="Allele Count (DPR ro AN) column"/>
             </when>
         </conditional>
-        <conditional name="ref_source">
-            <param name="index_source" type="select" label="Source for Genomic Data">
+        <conditional name="ref">
+            <param name="ref_source" type="select" label="Source for Genomic Data">
                 <option value="cached">Locally cached</option>
                 <option value="history">History</option>
             </param>
@@ -89,13 +90,13 @@
         
     </inputs>
     <outputs>
-        <data name="output" format="tabular" label="${input} report"/>
+        <data name="output" format="tabular" />
     </outputs>
     <tests>
         <test>
             <param name="fmt" value="vcf"/>
             <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
-            <param name="index_source" value="history"/>
+            <param name="ref_source" value="history"/>
             <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
             <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
             <output name="output_file">
@@ -108,7 +109,7 @@
         <test>
             <param name="fmt" value="vcf"/>
             <param name="input_vcf" value="GRCh38_X400k_EFF.vcf" ftype="vcf"/>
-            <param name="index_source" value="history"/>
+            <param name="ref_source" value="history"/>
             <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
             <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
             <output name="output_file">
@@ -121,7 +122,7 @@
         <test>
             <param name="fmt" value="vcf"/>
             <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
-            <param name="index_source" value="history"/>
+            <param name="ref_source" value="history"/>
             <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
             <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
             <param name="readthrough" value="1"/>
@@ -135,7 +136,7 @@
         <test>
             <param name="fmt" value="vcf"/>
             <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
-            <param name="index_source" value="history"/>
+            <param name="ref_source" value="history"/>
             <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
             <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
             <param name="min_depth" value="100"/>
@@ -150,7 +151,7 @@
         <test>
             <param name="fmt" value="tsv"/>
             <param name="input_tsv" value="GRCh38_X400k.tsv" ftype="tabular"/>
-            <param name="index_source" value="history"/>
+            <param name="ref_source" value="history"/>
             <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
             <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
             <param name="pos_column" value="2"/>