diff smalt_map.sh @ 0:77cc50d982c0 draft default tip

planemo upload for repository https://sourceforge.net/projects/smalt/ commit 008f4667b70be22e9ddf496738b3f74bb942ed28

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smalt_map.sh	Tue Sep 19 16:40:17 2017 -0400
@@ -0,0 +1,58 @@
+#/bin/bash
+
+
+smi=$1
+shift
+sma=$1
+shift
+#get format type so we can do extra work if it is a bam file
+format=$1
+shift
+
+#get working directory so we can find the output files 
+CUR_DIR=`pwd`
+
+
+cp "$smi" "$CUR_DIR/temp.smi"
+cp "$sma" "$CUR_DIR/temp.sma"
+
+#determine if we have 1 or 2
+num_inputs=$1
+shift
+
+inputs=()
+
+#determine how many fasta/fastq were given. Needs to be provided by user
+if [ $num_inputs -eq 1 ]; then
+    inputs+=$1
+    shift
+elif [ $num_inputs -eq 2 ]; then
+    inputs+=$1
+    shift
+    inputs+=' '
+    inputs+=$1
+    shift    
+else
+    exit 1
+fi
+
+smaltout=$2
+
+smalt map $@ 'temp' $inputs
+
+
+if [ "$format" == "bam" ]; then
+	if [ $GALAXY_SLOTS ]
+	then
+	    samtools sort -@ $GALAXY_SLOTS $smaltout 'temp2'
+	else
+	    samtools sort $smaltout 'temp2'
+	fi
+	mv 'temp2.bam' $smaltout
+fi
+
+#remove index files
+rm "$CUR_DIR/temp.smi"
+rm "$CUR_DIR/temp.sma"
+
+exit 0