Mercurial > repos > thondeboer > neat_genreads

diff genSeqErrorModel.xml @ 9:441103f02a11 draft

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planemo upload commit e96b43f96afce6a7b7dfd4499933aad7d05c955e-dirty
author thondeboer
date Wed, 16 May 2018 02:05:26 -0400
parents 5bcfac4f8116
children
line wrap: on
line diff
--- 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