diff srf2fastq/srf2fastq.sh @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/srf2fastq.sh	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,28 @@
+#!/bin/sh
+
+#change this if the path is different 
+convert=/usr/local/bin/srf2fastq
+
+srf_file=$1
+use_filter=$2
+use_paired=$3
+fastq_file1=$4
+fastq_file2=$5
+options='-c '
+
+if [ $use_filter == 'Y' ]
+then
+  options="$options -C"
+fi
+
+if [ $use_paired == 'Y' ]
+then
+  options="$options -n -a -s ${fastq_file1}"
+  ${convert} ${options} ${srf_file}
+  #after conversion rename files
+  mv ${fastq_file1}_1.fastq ${fastq_file1}
+  mv ${fastq_file1}_2.fastq ${fastq_file2}
+else
+  ${convert} ${options} ${srf_file} > ${fastq_file1}
+fi
+