diff --git a/gff2embl b/gff2embl index 1ef30690d67c5e2f57157cf27e8b4fc433de439c..6052ebde5d4745652f784dff6d7fd00c8554cc10 100755 --- a/gff2embl +++ b/gff2embl @@ -23,6 +23,34 @@ CLASSPATH=$ARTEMIS_HOME/lib/picard/sam.jar:$ARTEMIS_HOME/lib/picard/picard.jar:$ CLASSPATH="$ARTEMIS_HOME/lib/commons-lang-2.6.jar:$CLASSPATH" export CLASSPATH +if [ $# = 0 ] +then + : +else + if [ "$1" = "-h" -o "$1" = "--help" -o "$1" = "-help" ] + then + cat <<EOF + +SYNOPSIS + gff2embl +USAGE + $0 [options] <SEQUENCE_FILE> +OPTIONS + SEQUENCE_FILE A GFF3 file + + -s FILE space separated list of GFF files to read and write out + -o OUTPUT_DIR output directory + -f [y/n] flatten the gene model, default is y + -z gzip output, default is y + -a [y|n] for EMBL submission format change to n, default is y +EXAMPLES + % -s /Users/tjc/test.gff -o /Users/tjc +HOMEPAGE + http://www.sanger.ac.uk/resources/software/artemis/ +EOF + exit 0 + fi +fi ARTEMIS_PROPERTIES="-Dartemis.environment=UNIX"