[med-svn] [libncl] 03/03: Add manpages

Mon Jan 4 18:36:53 UTC 2016

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tille pushed a commit to branch master
in repository libncl.

commit 63841ae79d4e2d71c3ad135fd02e5f96556cbfa3
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jan 4 17:09:32 2016 +0100

    Add manpages
---
 debian/mans/NCLconverter.1    | 134 ++++++++++++++++++++++++++++++++++++++++++
 debian/mans/NEXUSnormalizer.1 | 113 +++++++++++++++++++++++++++++++++++
 debian/mans/NEXUSvalidator.1  | 111 ++++++++++++++++++++++++++++++++++
 debian/ncl-tools.manpages     |   1 +
 4 files changed, 359 insertions(+)

diff --git a/debian/mans/NCLconverter.1 b/debian/mans/NCLconverter.1
new file mode 100644
index 0000000..8686a87
--- /dev/null
+++ b/debian/mans/NCLconverter.1
@@ -0,0 +1,134 @@
+.TH NCLCONVERTER "1" "January 2016" "NCLconverter 2.1.18" "User Commands"
+.SH NAME
+NCLconverter \- report of content of NEXUS file
+.SH DESCRIPTION
+NCLconverter takes reads a file and writes a report of the content to a file prefix (specified with the \fB\-o\fR flag) in the chosen output format (specified with the \fB\-e\fR flag).
+.SS "The most common usage is simply:"
+.IP
+NCLconverter <path to NEXUS file>
+.SH OPTIONS
+.HP
+\fB\-h\fR on the command line shows this help message
+.HP
+\fB\-q\fR suppress NCL status messages while reading files
+.HP
+\fB\-l\fR<path> reads a file and treats each line of the file as a path to NEXUS file
+.HP
+\fB\-a\fR output AltNexus (no translation table in trees)
+.HP
+\fB\-x\fR do NOT validate internal labels in trees as taxa labels
+.HP
+\fB\-X\fR do NOT treat numbers in trees as taxon numbers, treat them as arbitrary
+.IP
+labels (should not be used with NEXUS files).
+.HP
+\fB\-s\fR<non\-negative integer> controls the NEXUS strictness level.
+.IP
+the default level is equivalent to \fB\-s2\fR invoking the program with
+\fB\-s3\fR or a higher number will convert some warnings into fatal errors.
+Running with \fB\-s1\fR will cause the parser to accept dangerous constructs,
+and running with \fB\-s0\fR will cause the parser make every attempt to finish
+parsing the file (warning about very serious errors).
+.IP
+Note that when \fB\-s0\fR strictness level is used, and the parser fails to
+finish, it will often be the result of an earlier error than the
+error that is reported in the last message.
+.HP
+\fB\-i\fR<number> specifies the length of the interleaved pages to create
+.HP
+\fB\-f\fR<format> specifies the input file format expected:
+.TP
+\fB\-fnexus\fR
+NEXUS (this is also the default)
+.TP
+\fB\-faafasta\fR
+Amino acid data in fasta
+.TP
+\fB\-fdnafasta\fR
+DNA data in fasta
+.TP
+\fB\-frnafasta\fR
+RNA data in fasta
+.IP
+The complete list of format names that can follow the \fB\-f\fR flag is:
+.IP
+nexus
+dnafasta
+aafasta
+rnafasta
+dnaphylip
+rnaphylip
+aaphylip
+discretephylip
+dnaphylipinterleaved
+rnaphylipinterleaved
+aaphylipinterleaved
+discretephylipinterleaved
+dnarelaxedphylip
+rnarelaxedphylip
+aarelaxedphylip
+discreterelaxedphylip
+dnarelaxedphylipinterleaved
+rnarelaxedphylipinterleaved
+aarelaxedphylipinterleaved
+discreterelaxedphylipinterleaved
+dnaaln
+rnaaln
+aaaln
+phyliptree
+relaxedphyliptree
+nexml
+dnafin
+aafin
+rnafin
+.HP
+\fB\-e\fR<format> specifies the output file format expected:
+.TP
+\fB\-enexus\fR
+"normalized" NEXUS output
+.TP
+\fB\-efasta\fR
+Character data in fasta (could result in multiple output files)
+.TP
+\fB\-ephylip\fR
+Trees and character data in phylip (could result in multiple output files)
+.TP
+\fB\-erelaxedphylip\fR
+Trees and character data in relaxed phylip (could result in multiple output files)
+.TP
+\fB\-enexml\fR
+nexml output (this is also the default)
+.TP
+\fB\-o\fR<fn> specifies the output prefix.
+An appropriate suffix and extension are added
+.HP
+\fB\-d\fR<fn> specifies the single output destination. Or you can use \fB\-d\-\fR to indicate that
+.IP
+output should be directed to standard output.Warning use of this option may result
+in an invalid output due to concatenation of separate "blocks" of information
+into a single file!
+.TP
+\fB\-u\fR
+converts underscores to spaces in formats other than NEXUS.
+.HP
+\fB\-y\fR<filename> translate to "safe" taxon names and store the new names as a NEXUS.
+.IP
+file called <filename> with a TaxaAssociation block. The first taxa block
+in the association block will hold the original names, and the second will
+hold the "safe" names
+.TP
+\fB\-Y\fR<filename> behaves like \fB\-y\fR, except with \fB\-Y\fR a translation file will be produced even
+if the original names were already "safe"
+.HP
+\fB\-z\fR<filename> use the NEXUS\-formatted file called <filename> with a TaxaAssociation block
+.TP
+to restore original names.
+Assumes that the first taxa block in the TaxaAssociation
+.IP
+block holds the original name and the second is the current name. This function
+is useful for "undoing" the effects of the \fB\-y\fR option.
+.TP
+\fB\-j\fR
+Suppress the creation of a NameTranslationFile
+.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/mans/NEXUSnormalizer.1 b/debian/mans/NEXUSnormalizer.1
new file mode 100644
index 0000000..b1e9a93
--- /dev/null
+++ b/debian/mans/NEXUSnormalizer.1
@@ -0,0 +1,113 @@
+.TH NEXUSNORMALIZER "1" "January 2016" "NEXUSnormalizer 2.1.18" "User Commands"
+.SH NAME
+NEXUSnormalizer \- rewrites NEXUS file to standard out with consistent indentation and syntax
+.SH DESCRIPTION
+NEXUSnormalizer takes reads a file and rewrites the file to standard out with consistent indentation and syntax.
+.SS "The most common usage is simply:"
+.IP
+NEXUSnormalizer <path to NEXUS file>
+.SH OPTIONS
+.HP
+\fB\-h\fR on the command line shows this help message
+.HP
+\fB\-q\fR suppress NCL status messages while reading files
+.HP
+\fB\-l\fR<path> reads a file and treats each line of the file as a path to NEXUS file
+.HP
+\fB\-a\fR output AltNexus (no translation table in trees)
+.HP
+\fB\-x\fR do NOT validate internal labels in trees as taxa labels
+.HP
+\fB\-X\fR do NOT treat numbers in trees as taxon numbers, treat them as arbitrary
+.IP
+labels (should not be used with NEXUS files).
+.HP
+\fB\-s\fR<non\-negative integer> controls the NEXUS strictness level.
+.IP
+the default level is equivalent to \fB\-s2\fR invoking the program with
+\fB\-s3\fR or a higher number will convert some warnings into fatal errors.
+Running with \fB\-s1\fR will cause the parser to accept dangerous constructs,
+and running with \fB\-s0\fR will cause the parser make every attempt to finish
+parsing the file (warning about very serious errors).
+.IP
+Note that when \fB\-s0\fR strictness level is used, and the parser fails to
+finish, it will often be the result of an earlier error than the
+error that is reported in the last message.
+.HP
+\fB\-i\fR<number> specifies the length of the interleaved pages to create
+.HP
+\fB\-f\fR<format> specifies the input file format expected:
+.TP
+\fB\-fnexus\fR
+NEXUS (this is also the default)
+.TP
+\fB\-faafasta\fR
+Amino acid data in fasta
+.TP
+\fB\-fdnafasta\fR
+DNA data in fasta
+.TP
+\fB\-frnafasta\fR
+RNA data in fasta
+.IP
+The complete list of format names that can follow the \fB\-f\fR flag is:
+.IP
+nexus
+.br
+dnafasta
+.br
+aafasta
+.br
+rnafasta
+.br
+dnaphylip
+.br
+rnaphylip
+.br
+aaphylip
+.br
+discretephylip
+.br
+dnaphylipinterleaved
+.br
+rnaphylipinterleaved
+.br
+aaphylipinterleaved
+.br
+discretephylipinterleaved
+.br
+dnarelaxedphylip
+.br
+rnarelaxedphylip
+.br
+aarelaxedphylip
+.br
+discreterelaxedphylip
+.br
+dnarelaxedphylipinterleaved
+.br
+rnarelaxedphylipinterleaved
+.br
+aarelaxedphylipinterleaved
+.br
+discreterelaxedphylipinterleaved
+.br
+dnaaln
+.br
+rnaaln
+.br
+aaaln
+.br
+phyliptree
+.br
+relaxedphyliptree
+.br
+nexml
+.br
+dnafin
+.br
+aafin
+.br
+rnafin
+.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/mans/NEXUSvalidator.1 b/debian/mans/NEXUSvalidator.1
new file mode 100644
index 0000000..0d6bb4e
--- /dev/null
+++ b/debian/mans/NEXUSvalidator.1
@@ -0,0 +1,111 @@
+.TH NEXUSVALIDATOR "1" "January 2016" "NEXUSvalidator 2.1.18" "User Commands"
+.SH NAME
+NEXUSvalidator \- validate NEXUS file
+.SH DESCRIPTION
+NEXUSvalidator takes reads a file and exits with a success (return code 0) if the file is valid.
+.SS "The most common usage is simply:"
+.IP
+NEXUSvalidator <path to NEXUS file>
+.SH OPTIONS
+.HP
+\fB\-h\fR on the command line shows this help message
+.HP
+\fB\-q\fR suppress NCL status messages while reading files
+.HP
+\fB\-l\fR<path> reads a file and treats each line of the file as a path to NEXUS file
+.HP
+\fB\-a\fR output AltNexus (no translation table in trees)
+.HP
+\fB\-x\fR do NOT validate internal labels in trees as taxa labels
+.HP
+\fB\-X\fR do NOT treat numbers in trees as taxon numbers, treat them as arbitrary
+.IP
+labels (should not be used with NEXUS files).
+.HP
+\fB\-s\fR<non\-negative integer> controls the NEXUS strictness level.
+.IP
+the default level is equivalent to \fB\-s2\fR invoking the program with
+\fB\-s3\fR or a higher number will convert some warnings into fatal errors.
+Running with \fB\-s1\fR will cause the parser to accept dangerous constructs,
+and running with \fB\-s0\fR will cause the parser make every attempt to finish
+parsing the file (warning about very serious errors).
+.IP
+Note that when \fB\-s0\fR strictness level is used, and the parser fails to
+finish, it will often be the result of an earlier error than the
+error that is reported in the last message.
+.HP
+\fB\-f\fR<format> specifies the input file format expected:
+.TP
+\fB\-fnexus\fR
+NEXUS (this is also the default)
+.TP
+\fB\-faafasta\fR
+Amino acid data in fasta
+.TP
+\fB\-fdnafasta\fR
+DNA data in fasta
+.TP
+\fB\-frnafasta\fR
+RNA data in fasta
+.IP
+The complete list of format names that can follow the \fB\-f\fR flag is:
+.IP
+nexus
+.br
+dnafasta
+.br
+aafasta
+.br
+rnafasta
+.br
+dnaphylip
+.br
+rnaphylip
+.br
+aaphylip
+.br
+discretephylip
+.br
+dnaphylipinterleaved
+.br
+rnaphylipinterleaved
+.br
+aaphylipinterleaved
+.br
+discretephylipinterleaved
+.br
+dnarelaxedphylip
+.br
+rnarelaxedphylip
+.br
+aarelaxedphylip
+.br
+discreterelaxedphylip
+.br
+dnarelaxedphylipinterleaved
+.br
+rnarelaxedphylipinterleaved
+.br
+aarelaxedphylipinterleaved
+.br
+discreterelaxedphylipinterleaved
+.br
+dnaaln
+.br
+rnaaln
+.br
+aaaln
+.br
+phyliptree
+.br
+relaxedphyliptree
+.br
+nexml
+.br
+dnafin
+.br
+aafin
+.br
+rnafin
+.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/ncl-tools.manpages b/debian/ncl-tools.manpages
new file mode 100644
index 0000000..4f4649b
--- /dev/null
+++ b/debian/ncl-tools.manpages
@@ -0,0 +1 @@
+debian/mans/*.1

-- 
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