# HG changeset patch
# User sanbi-uwc
# Date 1534756781 14400
# Node ID 51bc4a69349349bcc888c9701573fdd3535aec8e
# Parent  796bf12181f653835707f50296bfd8689d7d0d45
planemo upload for repository https://github.com/COMBAT-TB/vcf_snps_utils commit 738f22d38aa7721ccf5fb300f0185adac948beae

diff -r 796bf12181f6 -r 51bc4a693493 intersect.xml
--- a/intersect.xml	Thu Aug 16 17:02:25 2018 -0400
+++ b/intersect.xml	Mon Aug 20 05:19:41 2018 -0400
@@ -5,15 +5,17 @@
     <token name="@TOOL_VERSION@">0.0.2</token>
   </macros>
 
-  <requirements>
+   <requirements>
     <requirement type="package" version="@TOOL_VERSION@">vcf_snps_utils</requirement>
   </requirements>
         
   <command detect_errors="exit_code"><![CDATA[
     ln -s '$input_vcf' data.vcf &&
     ln -s '$input_csv' data.csv &&
-    vcf_snps_utils intersect data.vcf data.csv --out "$output_pdf.file.path"
-    ]]>
+    vcf_snps_utils intersect data.vcf data.csv --outdir "$output_pdf.files_path" &&
+    mv "$output_pdf.files_path"/Intervene_upset.pdf $output_pdf &&
+    mv "$output_pdf.files_path"/Intervene_upset_combinations.txt $output_txt
+    ]]>                                                                                                                 
   </command>
         
   <inputs>
@@ -24,7 +26,6 @@
   <outputs>
     <data name="output_pdf" format="pdf" label="SNPs Intersection Report" />
     <data name="output_txt" format="txt" label="SNPs Intersection Combination Report" />
-    <data name="output_r" format="R" label="SNPs Intersection R object" />
   </outputs>
         
   <tests>