# HG changeset patch
# User jpayne
# Date 1518631604 18000
# Node ID 1fe3b14f7f1b94a15f8a865f82b0604f0c82c90f
# Parent  a057e69d13a7ab83d5346e59681d2209ec694244
planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty

diff -r a057e69d13a7 -r 1fe3b14f7f1b 1_map_reads.xml
--- a/1_map_reads.xml	Mon Feb 05 13:25:39 2018 -0500
+++ b/1_map_reads.xml	Wed Feb 14 13:06:44 2018 -0500
@@ -7,6 +7,7 @@
         <!-- <requirement type="package" version="3.5">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        env &&
         #if $reads.reads_select == 'collection'
             export files="$reads.coll.forward $reads.coll.reverse"          &&
             export params="-1 $reads.coll.forward -2 $reads.coll.reverse"   &&
diff -r a057e69d13a7 -r 1fe3b14f7f1b 4_merge_sites.xml
--- a/4_merge_sites.xml	Mon Feb 05 13:25:39 2018 -0500
+++ b/4_merge_sites.xml	Wed Feb 14 13:06:44 2018 -0500
@@ -25,10 +25,10 @@
         <test>
             <param name="calls">
                 <collection type="list">
-                    <element name="sample1" value="samples/sample1/var.flt_preserved.vcf" />
-                    <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" />
-                    <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" />
-                    <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" />
+                    <element name="sample1" value="samples/sample1/var.flt_preserved.vcf" ftype="fastqsanger" />
+                    <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" ftype="fastqsanger" />
+                    <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" ftype="fastqsanger" />
+                    <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" ftype="fastqsanger" />
                 </collection>
             </param>
             <!-- <output name="snplist" value="snplist.txt" /> -->