# HG changeset patch
# User davidvanzessen
# Date 1481116629 18000
# Node ID c0ecc31829bd0d03088b52ec457e0fe3aa5c43da
# Parent  69baebd10e54433c64cc49c8b11b7e0381cba5de
Uploaded

diff -r 69baebd10e54 -r c0ecc31829bd gene_identification.py
--- a/gene_identification.py	Wed Dec 07 05:30:33 2016 -0500
+++ b/gene_identification.py	Wed Dec 07 08:17:09 2016 -0500
@@ -106,9 +106,6 @@
 
 for i in range(0, len(searchstrings["ce"]) - chunklength + 1, chunklength / 2):
   compiledregex["ce"].append((re.compile(searchstrings["ce"][i:i+chunklength]), False))
-  
-print "ce chunks", len(compiledregex["ce"])
-
 
 def removeAndReturnMaxIndex(x): #simplifies a list comprehension
   m = max(x)
diff -r 69baebd10e54 -r c0ecc31829bd shm_csr.xml
--- a/shm_csr.xml	Wed Dec 07 05:30:33 2016 -0500
+++ b/shm_csr.xml	Wed Dec 07 08:17:09 2016 -0500
@@ -1,7 +1,7 @@
 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0">
 	<description></description>
 	<command interpreter="bash">
-		wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast
+		wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast
 	</command>
 	<inputs>
 		<param name="in_file" type="data" label="IMGT zip file to be analysed" />
diff -r 69baebd10e54 -r c0ecc31829bd wrapper.sh
--- a/wrapper.sh	Wed Dec 07 05:30:33 2016 -0500
+++ b/wrapper.sh	Wed Dec 07 08:17:09 2016 -0500
@@ -10,15 +10,16 @@
 include_fr1=$6
 functionality=$7
 unique=$8
-naive_output_ca=$9
-naive_output_cg=${10}
-naive_output_cm=${11}
-naive_output_ce=${12}
-naive_output_all=${13}
-filter_unique=${14}
-class_filter=${15}
-empty_region_filter=${16}
-fast=${17}
+naive_output=$9
+naive_output_ca=${10}
+naive_output_cg=${11}
+naive_output_cm=${12}
+naive_output_ce=${13}
+naive_output_all=${14}
+filter_unique=${15}
+class_filter=${16}
+empty_region_filter=${17}
+fast=${18}
 mkdir $outdir
 
 tar -xzf $dir/style.tar.gz -C $outdir
@@ -701,10 +702,13 @@
 
 if [[ "$naive_output" == "yes" ]]
 then
+	echo "output naive output"
 	if [[ "${class_filter}" == "101_101" ]]
 	then
+		echo "copy new_IMGT.txz to ${naive_output_all}"
 		cp $outdir/new_IMGT.txz ${naive_output_all}
 	else
+		echo "copy for classes"
 		cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
 		cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
 		cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}