From 6b58bbeb7a5489b79462ac489ae27784e83f4592 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Mon, 18 Jun 2012 09:45:19 +0100
Subject: [PATCH] add help changes
---
art | 31 ++++++++++++++++++++++++++++++-
1 file changed, 30 insertions(+), 1 deletion(-)
mode change 100755 => 100644 art
diff --git a/art b/art
old mode 100755
new mode 100644
index f14081621..b4c6a1eca
--- 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
--
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