[med-svn] [sistr] 04/04: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository sistr.

commit d89cb221d7fac02e139d2fbfcee13d19b1696bf5
Author: Andreas Tille <tille at debian.org>
Date:   Wed Oct 11 21:03:16 2017 +0200

    Add manpage
---
 debian/manpages |  1 +
 debian/sistr.1  | 92 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 93 insertions(+)

diff --git a/debian/manpages b/debian/manpages
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+debian/*.1
diff --git a/debian/sistr.1 b/debian/sistr.1
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+.TH SISTR "1" "October 2017" "sistr 1.0.2" "User Commands"
+.SH NAME
+sistr \- SISTR (Salmonella In Silico Typing Resource) Command-line Tool
+.SH SYNOPSIS
+usage: sistr_cmd [\-h] [\-i fasta_path genome_name] [\-f OUTPUT_FORMAT]
+[\-o OUTPUT_PREDICTION] [\-M] [\-p CGMLST_PROFILES]
+[\-n NOVEL_ALLELES] [\-a ALLELES_OUTPUT] [\-T TMP_DIR] [\-K]
+[\-\-use\-full\-cgmlst\-db] [\-\-no\-cgmlst] [\-m] [\-\-qc] [\-t THREADS]
+[\-v] [\-V]
+[F [F ...]]
+.SH DESCRIPTION
+.SS SISTR (Salmonella In Silico Typing Resource) Command\-line Tool
+Serovar predictions from whole\-genome sequence assemblies by determination of antigen gene and cgMLST gene alleles using BLAST.
+.SH OPTIONS
+.SS "Note about using the "--use-full-cgmlst-db" flag:"
+.IP
+The "centroid" allele database is ~10% the size of the full set so analysis is much quicker with the "centroid" vs "full" set of alleles. Results between 2 cgMLST allele sets should not differ.
+.SS "positional arguments:"
+.TP
+F
+Input genome FASTA file
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-i\fR fasta_path genome_name, \fB\-\-input\-fasta\-genome\-name\fR fasta_path genome_name
+fasta file path to genome name pair
+.TP
+\fB\-f\fR OUTPUT_FORMAT, \fB\-\-output\-format\fR OUTPUT_FORMAT
+Output format (json, csv, pickle)
+.TP
+\fB\-o\fR OUTPUT_PREDICTION, \fB\-\-output\-prediction\fR OUTPUT_PREDICTION
+SISTR serovar prediction output path
+.TP
+\fB\-M\fR, \fB\-\-more\-results\fR
+Output more detailed results (\fB\-M\fR) and all antigen
+search blastn results (\fB\-MM\fR)
+.TP
+\fB\-p\fR CGMLST_PROFILES, \fB\-\-cgmlst\-profiles\fR CGMLST_PROFILES
+Output CSV file destination for cgMLST allelic
+profiles
+.TP
+\fB\-n\fR NOVEL_ALLELES, \fB\-\-novel\-alleles\fR NOVEL_ALLELES
+Output FASTA file destination of novel cgMLST alleles
+from input genomes
+.TP
+\fB\-a\fR ALLELES_OUTPUT, \fB\-\-alleles\-output\fR ALLELES_OUTPUT
+Output path of allele sequences and info to JSON
+.TP
+\fB\-T\fR TMP_DIR, \fB\-\-tmp\-dir\fR TMP_DIR
+Base temporary working directory for intermediate
+analysis files.
+.TP
+\fB\-K\fR, \fB\-\-keep\-tmp\fR
+Keep temporary analysis files.
+.TP
+\fB\-\-use\-full\-cgmlst\-db\fR
+Use the full set of cgMLST alleles which can include
+highly similar alleles. By default the smaller
+"centroid" alleles or representative alleles are used
+for each marker.
+.TP
+\fB\-\-no\-cgmlst\fR
+Do not run cgMLST serovar prediction
+.TP
+\fB\-m\fR, \fB\-\-run\-mash\fR
+Determine Mash MinHash genomic distances to Salmonella
+genomes with trusted serovar designations. Mash binary
+must be in accessible via $PATH (e.g. \fI\,/usr/bin\/\fP).
+.TP
+\fB\-\-qc\fR
+Perform basic QC to provide level of confidence in
+serovar prediction results.
+.TP
+\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
+Number of parallel threads to run sistr_cmd analysis.
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Logging verbosity level (\fB\-v\fR == show warnings; \fB\-vvv\fR ==
+show debug info)
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+show program's version number and exit
+.SH SEE ALSO
+If you find this program useful in your research, please cite as:
+.PP
+The Salmonella In Silico Typing Resource (SISTR): an open web\-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies.
+Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada.
+PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101
+.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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