diff --git a/art b/art old mode 100755 new mode 100644 index f14081621813e85b53c204853448452fe1842b38..b4c6a1eca3966872fc6532f6dc53d83c9e9dcab8 --- a/art +++ b/art @@ -83,7 +83,36 @@ else if [ "$1" = "-h" -o "$1" = "--help" -o "$1" = "-help" ] then cat <<EOF -usage: $0 [-options options_file] [EMBL/GENBANK/SEQUENCE_FILE [+FEATURE_FILE] [+FEATURE_FILE] ...] ... + +SYNOPSIS + Artemis: Genome Browser and Annotation Tool +USAGE + $0 [options] <SEQUENCE_FILE> [+FEATURE_FILE ...] +OPTIONS + SEQUENCE_FILE An EMBL, GenBank, FASTA, or GFF3 file + FEATURE_FILE An Artemis TAB file, or GFF file + + -quiet Suppress normal info messages while running + -options FILE Read a text file of options from FILE + -debug Run using the debugging JVM instead + -fast | -fast64 Use the FastVM (hp Tru64 UNIX) with 32/64 bit pointers + + -Dblack_belt_mode=? Keep warning messages to a minimum [true,false] + -Doffset=XXX Open viewer at base position XXX [integer >= 1] + -Duserplot=FILE[,FILE2] Open one or more userplots + -Dbam=FILE[,FILE2,...] Open one or more BAM, VCF or BCF files + -Dshow_forward_lines=? Hide/show forward frame lines [true,false] + -Dshow_reverse_lines=? Hide/show reverse frame lines [true,false] + -Dchado="h:p/d?u" Get Artemis to open this CHADO database + -Dread_only Open CHADO database read-only +EXAMPLES + % art AJ006275.embl + % art contigs.fa +annotation.gff +islands.tab + % art -Dblack_belt_mode=true -Dbam=ecoli_hiseq.bam E_coli_K12.gbk + % art -Duserplot=repeatmap.plot,geecee.plot Plasmid.gff3 +HOMEPAGE + http://www.sanger.ac.uk/resources/software/artemis/ + EOF exit 0 fi