diff falco-filter-report.sh @ 61:77979fe362c0 draft

Uploaded

--- a/falco-filter-report.sh	Fri Feb 27 06:31:30 2015 -0500
+++ b/falco-filter-report.sh	Fri Feb 27 06:53:34 2015 -0500
@@ -20,19 +20,19 @@
 ## ----------
 ## set params
 ## ----------
-if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default is "None" for some reason
-then 
-	FILTER_PARAM=" --filter "$filter_file
-else
-	FILTER_PARAM=""
-fi
+# if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default is "None" for some reason
+# then 
+# 	FILTER_PARAM=" --filter "$filter_file
+# else
+# 	FILTER_PARAM=""
+# fi
 
-if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" for some reason
-then 
-	MANIFEST_PARAM=" --manifest "$manifest_file
-else
-	MANIFEST_PARAM=""
-fi
+# if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" for some reason
+# then 
+# 	MANIFEST_PARAM=" --manifest "$manifest_file
+# else
+# 	MANIFEST_PARAM=""
+# fi
 
 ## name of file in galaxy not always set so will use a user-set job_name instead
 #bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
@@ -42,19 +42,19 @@
 ## Status / debug
 ## ----------
 DEBUG=1
-if [ $DEBUG ]
-then
-	DBS="[INFO] "
-	echo $DBS"FILTER:   "$filter_file
-	echo $DBS"MANIFEST: "$manifest_file
-	echo $DBS"REF FILE: "$REF_FILE
-	echo $DBS"DB KEY:   "$DB_KEY
-	echo $DBS"REF SRC:  "$REF_SOURCE
-	echo $DBS"BAM FILE: "$bam_file
-	echo $DBS"BAM NAME: "$bam_name
-	echo $DBS"BAM BASE: "$bam_base
-	echo $DBS"OUT PATH: "$out_path
-fi
+# if [ $DEBUG ]
+# then
+# 	DBS="[INFO] "
+# 	echo $DBS"FILTER:   "$filter_file
+# 	echo $DBS"MANIFEST: "$manifest_file
+# 	echo $DBS"REF FILE: "$REF_FILE
+# 	echo $DBS"DB KEY:   "$DB_KEY
+# 	echo $DBS"REF SRC:  "$REF_SOURCE
+# 	echo $DBS"BAM FILE: "$bam_file
+# 	echo $DBS"BAM NAME: "$bam_name
+# 	echo $DBS"BAM BASE: "$bam_base
+# 	echo $DBS"OUT PATH: "$out_path
+# fi
 
 ## ----------
 ## create output files dir