[med-svn] [ecopcr] 01/07: Manually formatting of manpages needed

Andreas Tille tille at debian.org
Thu Jun 25 09:57:58 UTC 2015 

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository ecopcr.

commit a60a02e79a6fc0ee577b711e3ab25e64c6e0dd67
Author: Andreas Tille <tille at debian.org>
Date:   Thu Jun 25 11:18:39 2015 +0200

    Manually formatting of manpages needed
---
 debian/man/ecoPCR.1          |  1 -
 debian/man/ecoPCRFormat.1    | 24 +++++++++++++----------
 debian/man/ecofind.1         | 46 +++++++++++++++++---------------------------
 debian/man/ecogrep.1         | 29 ++++++++++------------------
 debian/man/ecoisundertaxon.1 | 30 +++++++++++------------------
 5 files changed, 53 insertions(+), 77 deletions(-)

diff --git a/debian/man/ecoPCR.1 b/debian/man/ecoPCR.1
index 4e613b9..2033e11 100644
--- a/debian/man/ecoPCR.1
+++ b/debian/man/ecoPCR.1
@@ -1,4 +1,3 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
 .TH ECOPCR "1" "June 2015" "ecoPCR 0.5.0" "User Commands"
 .SH NAME
 ecoPCR \- searching for sequence and taxonomy hybriding with given primers
diff --git a/debian/man/ecoPCRFormat.1 b/debian/man/ecoPCRFormat.1
index 9de9021..1f5797d 100644
--- a/debian/man/ecoPCRFormat.1
+++ b/debian/man/ecoPCRFormat.1
@@ -1,22 +1,26 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
 .TH ECOPCRFORMAT "1" "June 2015" "ecoPCRFormat 0.5.0" "User Commands"
 .SH NAME
-ecoPCRFormat \- tool belonging to ecoPCR package
+ecoPCRFormat \- convert database into the format expected by ecoPCR
+.SH SYNOPSIS
+.B ecoPCRFormat
+\fB[option]\fR \fI<argument>\fR
 .SH DESCRIPTION
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-ecoPCRFormat
+ecoPCR is an electronic PCR software developed by LECA and
+Helix-Project. It helps to estimate Barcode primers quality.
 .PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-ecoPCRFormat [option] <argument>
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
+This program belongs to ecoPCR tools.
+.SH OPTIONS
+.TP
 \fB\-e\fR    \fB\-\-embl\fR        :[E]mbl format
+.TP
 \fB\-f\fR    \fB\-\-fasta\fR       :[F]asta format
+.TP
 \fB\-g\fR    \fB\-\-genbank\fR     :[G]enbank format
+.TP
 \fB\-h\fR    \fB\-\-help\fR        :[H]elp \- print this help
+.TP
 \fB\-n\fR    \fB\-\-name\fR        :[N]ame of the new database created
+.TP
 \fB\-t\fR    \fB\-\-taxonomy\fR    :[T]axonomy \- path to the taxonomy database
 .IP
 :bcp\-like dump from GenBank taxonomy database.
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
diff --git a/debian/man/ecofind.1 b/debian/man/ecofind.1
index a2b8bb2..36da55d 100644
--- a/debian/man/ecofind.1
+++ b/debian/man/ecofind.1
@@ -1,49 +1,39 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
 .TH ECOFIND "1" "June 2015" "ecofind 0.5.0" "User Commands"
 .SH NAME
 ecofind \- searching for taxonomic and rank and taxonomy id for given regular expression patterns
 .SH DESCRIPTION
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-ecofind Version 0.1
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-synopsis : searching for taxonomic and rank and
+ecoPCR is an electronic PCR software developed by LECA and
+Helix-Project. It helps to estimate Barcode primers quality.
+.PP
+This programm belongs to the exoPCR package.
+.SH SYNOPSIS
+.B ecofind
+\fB[options]\fR \fI<patterns>\fR
+.SH OPTIONS
 .TP
-taxonomy id for given regular
-expression patterns
-.PP
-usage: ecofind [options] <patterns>
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-options:
 \fB\-a\fR : [A]ll enable the search on all alternative names and not only scientific names.
-.PP
+.TP
 \fB\-d\fR : [D]atabase containing the taxonomy.
-.IP
 To match the expected format, the database
 has to be formated first by the ecoPCRFormat.py
 program located in the tools directory.
 Write the database radical without any extension.
-.PP
+.TP
 \fB\-h\fR : [H]elp \- print <this> help
-.PP
+.TP
 \fB\-l\fR : [L]ist all taxonomic rank available for \fB\-r\fR option
-.PP
+.TP
 \fB\-P\fR : [P]ath : add a column containing the full path for each displayed taxon
-.PP
+.TP
 \fB\-p\fR : [P]arents : specifiying this option displays all parental tree's information for the given taxid.
-.PP
+.TP
 \fB\-r\fR : [R]estrict to given taxonomic rank
-.PP
+.TP
 \fB\-s\fR : [S]ons: specifiying this option displays all subtree's information for the given taxid.
-.PP
+.TP
 \fB\-P\fR : Display taxonomic [P]ath as suplementary column in output
-.PP
+.TP
 arguments:
 <taxon> name pattern bearing regular expressions
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
+.SH SEE ALSO
 http://www.grenoble.prabi.fr/trac/ecoPCR/
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
diff --git a/debian/man/ecogrep.1 b/debian/man/ecogrep.1
index e97656d..4ceca48 100644
--- a/debian/man/ecogrep.1
+++ b/debian/man/ecogrep.1
@@ -1,21 +1,16 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
 .TH ECOGREP "1" "June 2015" "ecogrep 0.5.0" "User Commands"
 .SH NAME
 ecogrep \- filtering ecoPCR result based on taxonomic id filter and regular expression pattern
+.SH SYNOPSIS
+.B ecogrep
+\fB[options]\fR \fIfilename\fR
 .SH DESCRIPTION
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-ecogrep Version 0.1
+ecoPCR is an electronic PCR software developed by LECA and
+Helix-Project. It helps to estimate Barcode primers quality.
 .PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-synopsis : filtering ecoPCR result based on
-taxonomic id filter and regular expression pattern
-usage: ecogrep [options] filename
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-options:
+This programm belongs to the exoPCR package.
+.SH OPTIONS
+.TP
 \fB\-1\fR    : [FIRST] : compare the given pattern with direct strand oligonucleotide
 .TP
 \fB\-2\fR
@@ -41,12 +36,8 @@ options:
 .TP
 \fB\-v\fR
 : in[V]ert the sense of matching, to select non\-matching lines.
-.IP
+.TP
 argument:
 ecoPCR ouput file name
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
+.SH SEE ALSO
 http://www.grenoble.prabi.fr/trac/ecoPCR/
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
diff --git a/debian/man/ecoisundertaxon.1 b/debian/man/ecoisundertaxon.1
index bae4d51..68ca941 100644
--- a/debian/man/ecoisundertaxon.1
+++ b/debian/man/ecoisundertaxon.1
@@ -1,20 +1,16 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
 .TH ECOISUNDERTAXON "1" "June 2015" "ecoisundertaxon 0.5.0" "User Commands"
 .SH NAME
 ecoisundertaxon \- searching relationship in taxonomy
+.SH SYNOPSIS
+.B ecoisundertaxon
+\fB[options]\fR \fIdatabase\fR
 .SH DESCRIPTION
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-ecoisundertaxon Version 0.1
+ecoPCR is an electronic PCR software developed by LECA and
+Helix-Project. It helps to estimate Barcode primers quality.
 .PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-synopsis : searching relationship in taxonomy
-usage: ecoisundertaxon [options] database
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-options:
+This programm belongs to the exoPCR package.
+.SH OPTIONS
+.TP
 \fB\-1\fR    : [FIRST] taxomic id of the hypothetical son
 .TP
 \fB\-2\fR
@@ -26,13 +22,9 @@ options:
 \fB\-v\fR
 : [V]erbose mode. Display taxonomic information for both
 : taxonomic id.
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
+.TP
 database : to match the expected format, the database
 has to be formated first by the ecoPCRFormat.py program located.
 in the tools directory. Type the radical only, leaving out the extension
-.PP
-\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
-.IP
-https://www.grenoble.prabi.fr/trac/ecoPCR/wiki\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-
+.SH SEE ALSO
+https://www.grenoble.prabi.fr/trac/ecoPCR/wiki

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