[med-svn] [harvest-tools] 01/02: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository harvest-tools.

commit c7ef11ef9d884a6e1ce994d84508f4ec0f1d97c2
Author: Andreas Tille <tille at debian.org>
Date:   Tue Mar 15 14:40:36 2016 +0100

    Add manpage
---
 debian/control        | 10 ++++-----
 debian/harvesttools.1 | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/manpages       |  1 +
 3 files changed, 65 insertions(+), 5 deletions(-)

diff --git a/debian/control b/debian/control
index 833ae69..cd7d052 100644
--- a/debian/control
+++ b/debian/control
@@ -24,8 +24,8 @@ Depends: ${shlibs:Depends},
          ${misc:Depends}
 Description: archiving and postprocessing for reference-compressed genomic multi-alignments
  HarvestTools is a utility for creating and interfacing with Gingr files,
- which are efficient archives that the Harvest Suite uses to store reference-
- compressed multi-alignments, phylogenetic trees, filtered variants and
- annotations. Though designed for use with Parsnp and Gingr, HarvestTools
- can also be used for generic conversion between standard bioinformatics
- file formats.
+ which are efficient archives that the Harvest Suite uses to store
+ reference-compressed multi-alignments, phylogenetic trees, filtered
+ variants and annotations. Though designed for use with Parsnp and Gingr,
+ HarvestTools can also be used for generic conversion between standard
+ bioinformatics file formats.
diff --git a/debian/harvesttools.1 b/debian/harvesttools.1
new file mode 100644
index 0000000..1df46d4
--- /dev/null
+++ b/debian/harvesttools.1
@@ -0,0 +1,59 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
+.TH HARVESTTOOLS "1" "March 2016" "harvesttools 1.2" "User Commands"
+.SH NAME
+harvesttools \- archiving and postprocessing for reference-compressed genomic multi-alignments
+.SH SYNOPSIS
+.B harvesttools
+<options>
+.SH DESCRIPTION
+Harvesttools is a utility for creating and interfacing with Gingr files,
+which are efficient archives that the Harvest Suite uses to store
+reference-compressed multi-alignments, phylogenetic trees, filtered variants and
+annotations. Though designed for use with Parsnp and Gingr, HarvestTools
+can also be used for generic conversion between standard bioinformatics
+file formats.
+.SH OPTIONS
+.HP
+\fB\-i\fR <Gingr input>
+.HP
+\fB\-b\fR <bed filter intervals>,<filter name>,"<description>"
+.HP
+\fB\-B\fR <output backbone intervals>
+.HP
+\fB\-f\fR <reference fasta>
+.HP
+\fB\-F\fR <reference fasta out>
+.HP
+\fB\-g\fR <reference genbank>
+.HP
+\fB\-a\fR <MAF alignment input>
+.HP
+\fB\-m\fR <multi\-fasta alignment input>
+.HP
+\fB\-M\fR <multi\-fasta alignment output (concatenated LCBs)>
+.HP
+\fB\-n\fR <Newick tree input>
+.HP
+\fB\-N\fR <Newick tree output>
+.HP
+\fB\-\-midpoint\-reroot\fR (reroot the tree at its midpoint after loading)
+.HP
+\fB\-o\fR <Gingr output>
+.HP
+\fB\-S\fR <output for multi\-fasta SNPs>
+.HP
+\fB\-u\fR 0/1 (update the branch values to reflect genome length)
+.HP
+\fB\-v\fR <VCF input>
+.HP
+\fB\-V\fR <VCF output>
+.HP
+\fB\-x\fR <xmfa alignment file>
+.HP
+\fB\-X\fR <output xmfa alignment file>
+.HP
+\fB\-h\fR (show this help)
+.HP
+\fB\-q\fR (quiet mode)
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1

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