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commit a39a28548c45cdafd19d4eab64c9c39147435e8c Author: Afif Elghraoui <[email protected]> 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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbh5tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
