[med-svn] [parsnp] 02/02: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository parsnp.

commit 5fb2bfa755d56162056fc94d5617d263a3602678
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jul 21 09:14:37 2016 +0200

    Add manpage
---
 debian/manpages |  1 +
 debian/parsnp.1 | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 81 insertions(+)

diff --git a/debian/manpages b/debian/manpages
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+debian/*.1
diff --git a/debian/parsnp.1 b/debian/parsnp.1
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+.TH PARSNP "1" "July 2016" "parsnp 1.2" "User Commands"
+.SH NAME
+parsnp \- rapid core genome multi-alignment
+.SH SYNOPSIS
+.B parsnp
+[options] [\-g|\-r|\-q] \fB\-d\fR <genome_dir> \fB\-p\fR <threads>
+.SH DESCRIPTION
+Parsnp was designed to align the core genome of hundreds to thousands of
+bacterial genomes within a few minutes to few hours. Input can be both
+draft assemblies and finished genomes, and output includes variant (SNP)
+calls, core genome phylogeny and multi-alignments. Parsnp leverages
+contextual information provided by multi-alignments surrounding SNP
+sites for filtration/cleaning, in addition to existing tools for
+recombination detection/filtration and phylogenetic reconstruction.
+.SH OPTIONS
+.SS input/output
+.HP
+\fB\-c\fR = <flag>: (c)urated genome directory, use all genomes in dir and ignore MUMi? (default = NO)
+.HP
+\fB\-d\fR = <path>: (d)irectory containing genomes/contigs/scaffolds
+.HP
+\fB\-r\fR = <path>: (r)eference genome (set to ! to pick random one from genome dir)
+.HP
+\fB\-g\fR = <string>: Gen(b)ank file(s) (gbk), comma separated list (default = None)
+.HP
+\fB\-o\fR = <string>: output directory? default [./P_CURRDATE_CURRTIME]
+.HP
+\fB\-q\fR = <path>: (optional) specify (assembled) query genome to use, in addition to genomes found in genome dir (default = NONE)
+.SS MUMi
+.HP
+\fB\-U\fR = <float>: max MUMi distance value for MUMi distribution
+.HP
+\fB\-M\fR = <flag>: calculate MUMi and exit? overrides all other choices! (default: NO)
+.HP
+\fB\-i\fR = <float>: max MUM(i) distance (default: autocutoff based on distribution of MUMi values)
+.SS MUM search
+.HP
+\fB\-a\fR = <int>: min (a)NCHOR length (default = 1.1*Log(S))
+.HP
+\fB\-C\fR = <int>: maximal cluster D value? (default=100)
+.HP
+\fB\-z\fR = <path>: min LCB si(z)e? (default = 25)
+.SS LCB alignment
+.HP
+\fB\-D\fR = <float>: maximal diagonal difference? Either percentage (e.g. 0.2) or bp (e.g. 100bp) (default = 0.12)
+.HP
+\fB\-e\fR = <flag> greedily extend LCBs? experimental! (default = NO)
+.HP
+\fB\-n\fR = <string>: alignment program (default: libMUSCLE)
+.HP
+\fB\-u\fR = <flag>: output unaligned regions? .unaligned (default: NO)
+.SS Recombination filtration
+.HP
+\fB\-x\fR = <flag>: enable filtering of SNPs located in PhiPack identified regions of recombination? (default: NO)
+.SS Misc
+.HP
+\fB\-h\fR = <flag>: (h)elp: print this message and exit
+.HP
+\fB\-p\fR = <int>: number of threads to use? (default= 1)
+.HP
+\fB\-P\fR = <int>: max partition size? limits memory usage (default= 15000000)
+.HP
+\fB\-v\fR = <flag>: (v)erbose output? (default = NO)
+.HP
+\fB\-V\fR = <flag>: output (V)ersion and exit
+.SH EXAMPLES
+Parsnp quick start for three example scenarios:
+.SS With reference & genbank file:
+.IP
+parsnp \fB\-g\fR <reference_genbank_file1,reference_genbank_file2,..> \fB\-d\fR <genome_dir> \fB\-p\fR <threads>
+.SS With reference but without genbank file:
+.IP
+parsnp \fB\-r\fR <reference_genome> \fB\-d\fR <genome_dir> \fB\-p\fR <threads>
+.SS Autorecruit reference to a draft assembly:
+.IP
+parsnp \fB\-q\fR <draft_assembly> \fB\-d\fR <genome_db> \fB\-p\fR <threads>
+.SH SEE ALSO
+For detailed documentation please see \fB\-\-\fR> http://harvest.readthedocs.org/en/latest
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

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