--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/weeder2_wrapper.sh	Wed Nov 19 07:56:27 2014 -0500
@@ -0,0 +1,62 @@
+#!/bin/sh -e
+#
+# Wrapper script to run weeder2 as a Galaxy tool
+#
+# Usage: weeder_wrapper.sh FASTA_IN SPECIES_CODE MOTIFS_OUT MATRIX_OUT [ ARGS... ]
+#
+# ARGS: one or more arguments to supply directly to weeder2
+#
+# Process command line
+FASTA_IN=$1
+SPECIES_CODE=$2
+MOTIFS_OUT=$3
+MATRIX_OUT=$4
+#
+# Other arguments
+ARGS=""
+while [ ! -z "$5" ] ; do
+    ARGS="$ARGS $5"
+    shift
+done
+#
+# Link to input file
+ln -s $FASTA_IN
+#
+# Link to the FreqFiles directory as weeder2 executable
+# expects it to be the same directory
+freqfiles_dir=$WEEDER_FREQFILES_DIR
+if [ -d $freqfiles_dir ] ; then
+    echo "Linking to FreqFiles directory"
+    ln -s $freqfiles_dir FreqFiles
+else
+    echo "ERROR FreqFiles directory not found" >&2
+    exit 1
+fi
+#
+# Construct names of input and output files
+fasta=`basename $FASTA_IN`
+motifs_out=$fasta.w2
+matrix_out=$fasta.matrix.w2
+#
+# Construct and run weeder command
+# NB weeder logs output to stderr so redirect to stdout
+# to prevent the Galaxy tool reporting failure
+weeder_cmd="weeder2 -f $fasta -O $SPECIES_CODE $ARGS"
+echo "Running $weeder_cmd"
+$weeder_cmd 2>&1
+status=$?
+if [ $status -ne 0 ] ; then
+    echo weeder2 command finished with nonzero exit code $status >&2
+    echo Command was: $weeder_cmd
+    exit $status
+fi
+#
+# Move outputs to final destinations
+if [ -e $motifs_out ] ; then
+    /bin/mv $motifs_out $MOTIFS_OUT
+fi
+if [ -e $matrix_out ] ; then
+    /bin/mv $matrix_out $MATRIX_OUT
+fi
+#
+# Done