[med-svn] [artemis] 03/13: Add manpage for art based on upstream's wrapper script help

[Afif Elghraoui]

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commit 20e1dfc484cddb18c8ffb5169d1e79ffcf065bb8
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu Oct 22 19:27:30 2015 -0700

    Add manpage for art based on upstream's wrapper script help
---
 debian/artemis.manpages |  1 +
 debian/man/art.1        | 41 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+)

diff --git a/debian/artemis.manpages b/debian/artemis.manpages
new file mode 100644
index 0000000..5062b97
--- /dev/null
+++ b/debian/artemis.manpages
@@ -0,0 +1 @@
+debian/man/art.1
diff --git a/debian/man/art.1 b/debian/man/art.1
new file mode 100644
index 0000000..fe6ccd6
--- /dev/null
+++ b/debian/man/art.1
@@ -0,0 +1,41 @@
+.TH ART 1 "February 2014"
+
+.SH NAME
+art \- Artemis genome browser and annotation tool
+
+.SH SYNOPSIS
+.B art
+.RI [ options ]
+.I SEQUENCE_FILE
+.RI [ +FEATURE_FILE ...]
+
+.SH OPTIONS
+        SEQUENCE_FILE                  An EMBL, GenBank, FASTA, or GFF3 file
+        FEATURE_FILE                   An Artemis TAB file, or GFF file
+
+        -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
+        -Dloguserplot=FILE[,FILE2]     Open one or more userplots, take log(data)
+        -Dbam=FILE[,FILE2,...]         Open one or more BAM, VCF or BCF files
+        -DbamClone=n                   Open all BAMs in multiple (n > 1) panels
+        -Dbam[1,2,..]=FILE[,FILE2,..]  Open BAMs in separate panels
+        -Dshow_snps                    Show SNP marks in BamView
+        -Dshow_snp_plot                Open SNP plot in BamView
+        -Dshow_cov_plot                Open coverage plot in BamView
+        -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
+.SH 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
+.SH HOMEPAGE
+        http://www.sanger.ac.uk/resources/software/artemis/
+

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