# HG changeset patch
# User greg
# Date 1543951927 18000
# Node ID 85da3036bd6aa1b85b6d68073c0e6f2f3d0f7819
# Parent  b37deda778b9333eddcede48ab7dc2ad8b86b2ab
Uploaded

diff -r b37deda778b9 -r 85da3036bd6a affy_ids_for_genotyping.xml
--- a/affy_ids_for_genotyping.xml	Tue Dec 04 14:20:10 2018 -0500
+++ b/affy_ids_for_genotyping.xml	Tue Dec 04 14:32:07 2018 -0500
@@ -1,9 +1,9 @@
 <tool id="affy_ids_for_genotyping" name="Extract Affymetrix ids for genotyping" version="1.0.0">
     <description>from VCF data</description>
     <command detect_errors="exit_code"><![CDATA[
-grep "#CHROM" '$input_vcf' > test.head
-tr '\t' '\n' < test.head > samples.txt
-sed -i 1,9d samples.txt
+grep "#CHROM" '$input_vcf' > test.head &&
+tr '\t' '\n' < test.head > samples.txt &&
+sed -i 1,9d samples.txt &&
 awk -F'\t' -v OFS='\t' 'NR==0 {print ; next}{print (NR),$0}' samples.txt > '$output'
 ]]></command>
     <inputs>