# HG changeset patch
# User thondeboer
# Date 1526450726 14400
# Node ID 441103f02a1199636d8e0dcbabe1c0c453062299
# Parent  dc383ecbf839fc152b8fa1e3ec37fc8b5b745e6b
planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty

diff -r dc383ecbf839 -r 441103f02a11 computeGC.xml
--- a/computeGC.xml	Tue May 15 23:09:17 2018 -0400
+++ b/computeGC.xml	Wed May 16 02:05:26 2018 -0400
@@ -15,8 +15,8 @@
 		#else:
 		  -g ${in_type.reference}
 		#end if
-		> out.genomecov
-	&& python2 $__tool_directory__/utilities/computeGC.py
+		> out.genomecov;
+	python2 $__tool_directory__/utilities/computeGC.py
 		#if $in_type.input_type == "built-in":
 		  -r ${in_type.reference.fields.path}
 		#else:
diff -r dc383ecbf839 -r 441103f02a11 genMutModel.xml
--- a/genMutModel.xml	Tue May 15 23:09:17 2018 -0400
+++ b/genMutModel.xml	Wed May 16 02:05:26 2018 -0400
@@ -10,13 +10,13 @@
   <command detect_errors="exit_code">
     <![CDATA[
 	## Filenames and extensions are important, so make some links to make life easier downstream
-	ln -s $mutation_file mutation_file.vcf
+	ln -s $mutation_file mutation_file.vcf;
 	#if $in_type.input_type == "built-in":
-	&& ln -s ${in_type.reference.fields.path} reference.fa
+	ln -s ${in_type.reference.fields.path} reference.fa;
 	#else:
-	&& ln -s ${in_type.reference} reference.fa
+	ln -s ${in_type.reference} reference.fa;
 	#end if
-    && python2 $__tool_directory__/utilities/genMutModel.py
+    python2 $__tool_directory__/utilities/genMutModel.py
 		-r reference.fa
 		-m mutation_file.vcf
 		-o $genMutModel_modelfile
diff -r dc383ecbf839 -r 441103f02a11 genSeqErrorModel.xml
--- a/genSeqErrorModel.xml	Tue May 15 23:09:17 2018 -0400
+++ b/genSeqErrorModel.xml	Wed May 16 02:05:26 2018 -0400
@@ -10,21 +10,21 @@
   <command detect_errors="exit_code">
     <![CDATA[
 	#if $lib_type_cond.read1.ext == "fastqsanger.gz":
-	  ln -s $lib_type_cond.read1 read1.fq.gz
+	  ln -s $lib_type_cond.read1 read1.fq.gz;
 	  #set $read1="read1.fq.gz"
 	  #if $lib_type_cond.lib_type == 'paired':
-	    && ln -s $lib_type_cond.read2 read2.fq.gz
+	    ln -s $lib_type_cond.read2 read2.fq.gz;
 		#set $read2="read2.fq.gz"
 	  #end if
 	#else
-	  ln -s $lib_type_cond.read1 read1.fq
+	  ln -s $lib_type_cond.read1 read1.fq;
 	  #set $read1="read1.fq"
 	  #if $lib_type_cond.lib_type == 'paired':
-	    && ln -s $lib_type_cond.read2 read2.fq
+	    ln -s $lib_type_cond.read2 read2.fq;
 		#set $read2="read2.fq"
 	  #end if
 	#end if
-	&& python2 $__tool_directory__/utilities/genSeqErrorModel.py
+	python2 $__tool_directory__/utilities/genSeqErrorModel.py
 	  -i $read1
 	#if $lib_type_cond.lib_type == 'paired':
 	  -i2 $read2