[med-svn] [python-pbh5tools] 07/07: manpages generated by help2man

[Afif Elghraoui]

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commit a39a28548c45cdafd19d4eab64c9c39147435e8c
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Aug 14 22:52:05 2015 -0700

    manpages generated by help2man
---
 debian/bash5tools.1 | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/cmph5tools.1 | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 113 insertions(+)

diff --git a/debian/bash5tools.1 b/debian/bash5tools.1
new file mode 100644
index 0000000..cc70c95
--- /dev/null
+++ b/debian/bash5tools.1
@@ -0,0 +1,56 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH BASH5TOOLS "1" "August 2015" "bash5tools 0.8.0" "User Commands"
+.SH NAME
+bash5tools \- manual page for bash5tools 0.8.0
+.SH DESCRIPTION
+usage: bash5tools [\-h] [\-\-verbose] [\-\-version] [\-\-profile] [\-\-debug]
+.IP
+[\-\-outFilePrefix OUTFILEPREFIX]
+[\-\-readType {ccs,subreads,unrolled}] [\-\-outType OUTTYPE]
+[\-\-minLength MINLENGTH] [\-\-minReadScore MINREADSCORE]
+[\-\-minPasses MINPASSES]
+input.bas.h5
+.PP
+Tool for extracting data from .bas.h5 files
+.SS "positional arguments:"
+.TP
+input.bas.h5
+input .bas.h5 filename
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-verbose\fR, \fB\-v\fR
+Set the verbosity level (default: None)
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-\-profile\fR
+Print runtime profile at exit (default: False)
+.TP
+\fB\-\-debug\fR
+Catch exceptions in debugger (requires ipdb) (default:
+False)
+.TP
+\fB\-\-outFilePrefix\fR OUTFILEPREFIX
+output filename prefix [None]
+.TP
+\fB\-\-readType\fR {ccs,subreads,unrolled}
+read type (ccs, subreads, or unrolled) []
+.TP
+\fB\-\-outType\fR OUTTYPE
+output file type (fasta, fastq) [fasta]
+.SS "Read filtering arguments:"
+.TP
+\fB\-\-minLength\fR MINLENGTH
+min read length [0]
+.TP
+\fB\-\-minReadScore\fR MINREADSCORE
+min read score, valid only with
+\fB\-\-readType=\fR{unrolled,subreads} [0]
+.TP
+\fB\-\-minPasses\fR MINPASSES
+min number of CCS passes, valid only with
+\fB\-\-readType\fR=\fI\,ccs\/\fR [0]
diff --git a/debian/cmph5tools.1 b/debian/cmph5tools.1
new file mode 100644
index 0000000..cbb7101
--- /dev/null
+++ b/debian/cmph5tools.1
@@ -0,0 +1,57 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
+.TH CMPH5TOOLS "1" "August 2015" "cmph5tools 0.8.0" "User Commands"
+.SH NAME
+cmph5tools \- manual page for cmph5tools 0.8.0
+.SH DESCRIPTION
+usage: cmph5tools [\-h] [\-\-verbose] [\-\-version] [\-\-profile] [\-\-debug]
+.IP
+{select,merge,sort,equal,summarize,stats,listMetrics,validate}
+\&...
+.PP
+Toolkit for command\-line tools associated with cmp.h5 file processing. Notes:
+For all command\-line arguments, default values are listed in [].
+.SS "positional arguments:"
+.IP
+{select,merge,sort,equal,summarize,stats,listMetrics,validate}
+.TP
+select
+Create new cmp.h5 files from selections of
+input.cmp.h5
+.TP
+merge
+Merge input.cmp.h5 files into out.cmp.h5
+.TP
+sort
+Sort input.cmp.h5 file
+.TP
+equal
+Compare two cmp.h5 files for equivalence
+.TP
+summarize
+Summarize contents of cmp.h5 files
+.TP
+stats
+Compute statistics from input.cmp.h5
+.TP
+listMetrics
+List available metrics
+.TP
+validate
+Validate input.cmp.h5
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-verbose\fR, \fB\-v\fR
+Set the verbosity level (default: None)
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-\-profile\fR
+Print runtime profile at exit (default: False)
+.TP
+\fB\-\-debug\fR
+Catch exceptions in debugger (requires ipdb) (default:
+False)

-- 
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