[med-svn] [arden] 01/01: Write manpages based on help2man
Andreas Tille
tille at debian.org
Fri Feb 7 15:12:13 UTC 2014
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository arden.
commit 2755d5fba352f9848460a048278ebc7bd4fcf587
Author: Andreas Tille <tille at debian.org>
Date: Fri Feb 7 16:17:19 2014 +0100
Write manpages based on help2man
---
debian/createmanpages | 9 ++++++
debian/manpages | 1 +
debian/mans/arden-analyze.1 | 32 ++++++++++++++++++++++
debian/mans/arden-create.1 | 67 +++++++++++++++++++++++++++++++++++++++++++++
debian/mans/arden-filter.1 | 40 +++++++++++++++++++++++++++
debian/rules | 6 ----
6 files changed, 149 insertions(+), 6 deletions(-)
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..3c9b381
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,9 @@
+help2man --no-info --no-discard-stderr \
+ --name='analyze the results of the artificial reference genome mapping' \
+ --version-string="2013-04-25" arden-analyze > debian/arden-analyze.1
+help2man --no-info --no-discard-stderr \
+ --name='generate an artificial reference genome (AR) from a given input' \
+ --version-string="2013-04-25" arden-create > debian/arden-create.1
+help2man --no-info --no-discard-stderr \
+ --name='filter a SAM file based on the analysis with ARDEN' \
+ --version-string="2013-04-25" arden-filter > debian/arden-filter.1
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..63ab24a
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*
diff --git a/debian/mans/arden-analyze.1 b/debian/mans/arden-analyze.1
new file mode 100644
index 0000000..41b0999
--- /dev/null
+++ b/debian/mans/arden-analyze.1
@@ -0,0 +1,32 @@
+.TH ARDEN-ANALYZE "1" "February 2014" "arden-analyze 2013-04-25" "User Commands"
+.SH NAME
+arden-analyze \- analyze the results of the artificial reference genome mapping
+.SH SYNOPSIS
+.B arden-analyze
+[\fIoptions\fR] [\fIINPUT FILE\fR] [\fIOUTPUTFOLDER\fR] ...
+.SH DESCRIPTION
+.P
+Script to analyze the results of the artificial reference genome mapping. This script identifies the putative TPs / FPs
+on a specific data set (reads).
+.SH OPTIONS
+.TP
+\fIOUTPUTFOLDER\fR
+path to output destination folder.
+.TP
+\fIINPUT FILE\fR
+ppath to ini file. To get the required format have a look at the example files.
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-p\fR PHRED, \fB\-\-phred\fR=\fIPHRED\fR
+Specify the PHRED encoding of the input reads i.e.
+Illumina 1.3+ = \fB\-p\fR 33.[default: 33]
+.TP
+\fB\-r\fR RANK, \fB\-\-internalrank\fR=\fIRANK\fR
+Use internal ranking for reads (needed if the read
+names cannot be lexicographically be sorted in the
+same way in python and your OS by sam tools).[default:1]
diff --git a/debian/mans/arden-create.1 b/debian/mans/arden-create.1
new file mode 100644
index 0000000..ad36362
--- /dev/null
+++ b/debian/mans/arden-create.1
@@ -0,0 +1,67 @@
+.TH ARDEN-CREATE "1" "February 2014" "arden-create 2013-04-25" "User Commands"
+.SH NAME
+arden-create \- generate an artificial reference genome (AR) from a given input
+.SH SYNOPSIS
+.B arden-create
+[\fIoptions\fR] [\fIOUTPUTFOLDER\fR] [\fIINPUT FASTA\fR]...
+.SH DESCRIPTION
+Script to generate an artificial reference genome (AR) from a given input. The AR fullfills
+the following conditions by default settings:
+.nr step 1 1
+.IP \n[step] 4
+has a nucleotide distribution equal to the input genome
+.IP \n+[step]
+has an amino acid (aa) distribution equal to the input genome
+.IP \n+[step]
+keeps the aa neighborhood similar to the neighborhood in input genome
+.IP \n+[step]
+protects start and stop codons from mutations
+.SH OPTIONS
+.P
+Required Arguments:
+.TP
+\fIOUTPUTFOLDER\fR
+complete path to output destination folder
+.TP
+\fIINPUT FASTA\fR
+Single sequence Fasta file.
+.IP
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-d\fR DISTANCE, \fB\-\-distance\fR=\fIDISTANCE\fR
+distance between 2 mutations on DNA level. The minimum
+distance will then be d\-3. [default: 15]
+.TP
+\fB\-o\fR ORF, \fB\-\-orf\fR=\fIORF\fR
+1\- protect ORF structure from mutations. 0 \- allow
+mutations in start / stop codon [default: 1]
+.TP
+\fB\-r\fR REVSUB, \fB\-\-revsub\fR=\fIREVSUB\fR
+1 \- reverse substitution if no suitable counterpart
+was found (balanced mutation). 0 \- keep the unbalanced
+mutations.[default: 1]
+.TP
+\fB\-m\fR RANDOM, \fB\-\-random\fR=\fIRANDOM\fR
+1/0 variable. 1 \- shuffled starting positions for the
+.IP
+mutations. 0 \- linear mutation [default: 1]
+.TP
+\fB\-s\fR SORF, \fB\-\-saveorfs\fR=\fISORF\fR
+Save found start and stop codons in a pickle file (can
+be loaded if the input fasta is used again if a
+filename is specified). [default: ]
+.TP
+\fB\-l\fR LORF, \fB\-\-loadorfs\fR=\fILORF\fR
+Specify filename to a previously created pickle file
+(contains positions of start/stop codons) [default: ]
+.TP
+\fB\-n\fR NAME, \fB\-\-name\fR=\fINAME\fR
+Specify name which will be used as header. [default: ]
+.TP
+\fB\-p\fR PEXAMPLES, \fB\-\-pexamples\fR=\fIPEXAMPLES\fR
+set to 1 if you want to print examples
diff --git a/debian/mans/arden-filter.1 b/debian/mans/arden-filter.1
new file mode 100644
index 0000000..da22cf9
--- /dev/null
+++ b/debian/mans/arden-filter.1
@@ -0,0 +1,40 @@
+.TH ARDEN-FILTER "1" "February 2014" "arden-filter 2013-04-25" "User Commands"
+.SH NAME
+arden-filter \- filter a SAM file based on the analysis with ARDEN
+.SH SYNOPSIS
+.B arden-filter
+[\fIINPUT SAM\fR] [\fIOUTPUTFILE\fR] [\fIOPTIONS\fR]...
+.SH DESCRIPTION
+.P
+Script to filter and a SAM file based on the analysis with ARDEN. It is necessary to specify the desired cutoffs for RQS,GAPS and MM.
+Type: python filter \fB\-e\fR 1 for printing some examples.
+.SH OPTIONS
+.P
+Required Arguments:
+.TP
+\fIOUTPUTFILE\fR
+Outputfilename
+.TP
+\fIINPUT\fR
+Single SAM file to filter.
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-r\fR RQS, \fB\-\-rqs\fR=\fIRQS\fR
+Threshold for minimum read quality score.. [default:
+0]
+.TP
+\fB\-m\fR MM, \fB\-\-mismatches\fR=\fIMM\fR
+Threshold for maximum number of mismatches in an
+alignment [default: 3]
+.TP
+\fB\-g\fR GAPS, \fB\-\-gaps\fR=\fIGAPS\fR
+Threshold for maximum number of gaps in an alignment.
+[default: 3]
+.TP
+\fB\-e\fR PEXAMPLES, \fB\-\-examples\fR=\fIPEXAMPLES\fR
+set to 1 if you want to print examples
diff --git a/debian/rules b/debian/rules
index b24c46a..7d11dde 100755
--- a/debian/rules
+++ b/debian/rules
@@ -6,9 +6,3 @@ DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
%:
dh $@ --with python2
-
-#override_dh_install:
-# dh_install
-# touch debian/$(DEBPKGNAME)/usr/share/pyshared/$(DEBPKGNAME)/__init__.py
-# touch debian/$(DEBPKGNAME)/usr/share/pyshared/$(DEBPKGNAME)/core/__init__.py
-
--
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