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commit d56943e00520de07b4230b04b824710fde51e046 Author: Andreas Tille <[email protected]> Date: Wed Jun 24 21:35:05 2015 +0200 Manpage for ecoisundertaxon; manually formatted ecoPCR.1 --- debian/createmanpages | 3 ++ debian/man/ecoPCR.1 | 86 ++++++++++++++++++++++++-------------------- debian/man/ecoisundertaxon.1 | 38 ++++++++++++++++++++ 3 files changed, 89 insertions(+), 38 deletions(-) diff --git a/debian/createmanpages b/debian/createmanpages index d0ab362..ecd3101 100755 --- a/debian/createmanpages +++ b/debian/createmanpages @@ -14,6 +14,9 @@ help2man --no-info --no-discard-stderr --help-option="-h" \ --name='filtering ecoPCR result based on taxonomic id filter and regular expression pattern' \ --version-string="$VERSION" ecogrep > $MANDIR/ecogrep.1 help2man --no-info --no-discard-stderr --help-option="-h" \ + --name='searching relationship in taxonomy' \ + --version-string="$VERSION" ecoisundertaxon > $MANDIR/ecoisundertaxon.1 +help2man --no-info --no-discard-stderr --help-option="-h" \ --name='tool belonging to ecoPCR package' \ --version-string="$VERSION" ecoPCRFormat > $MANDIR/ecoPCRFormat.1 sed -i 's/ecoPCRFormat\.py/ecoPCRFormat/g' $MANDIR/ecoPCRFormat.1 diff --git a/debian/man/ecoPCR.1 b/debian/man/ecoPCR.1 index 26ddaef..4e613b9 100644 --- a/debian/man/ecoPCR.1 +++ b/debian/man/ecoPCR.1 @@ -2,95 +2,105 @@ .TH ECOPCR "1" "June 2015" "ecoPCR 0.5.0" "User Commands" .SH NAME ecoPCR \- searching for sequence and taxonomy hybriding with given primers +.SH SYNOPSIS +.B ecoPCR +\fB[options]\fR \fI<nucleotidic patterns>\fR .SH DESCRIPTION -\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR -.IP -ecoPCR Version 0.2 -.PP -\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR -synopsis : searching for sequence and taxonomy hybriding with given primers -usage: ecoPCR [options] <nucleotidic patterns> -\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR -options: +ecoPCR is an electronic PCR software developed by LECA and +Helix-Project. It helps to estimate Barcode primers quality. +.SH OPTIONS +.TP \fB\-a\fR : Salt concentration in M for Tm computation (default 0.05 M) -.PP +.TP \fB\-c\fR : Consider that the database sequences are [c]ircular -.PP +.TP \fB\-d\fR : [D]atabase : to match the expected format, the database -.IP -has to be formated first by the ecoPCRFormat.py program located. -in the tools directory. -ecoPCRFormat.py creates three file types : +has to be formated first by the ecoPCRFormat(1) program. +ecoPCRFormat(1) creates three file types: .IP \&.sdx : contains the sequences +.IP \&.tdx : contains information concerning the taxonomy +.IP \&.rdx : contains the taxonomy rank .IP ecoPCR needs all the file type. As a result, you have to write the database radical without any extension. For example \fI\,/ecoPCRDB/gbmam\/\fP -.PP +.TP \fB\-D\fR : Keeps the specified number of nucleotides on each side of the in silico -.IP amplified sequences (including the amplified DNA fragment plus the two target sequences of the primers). -.PP +.TP \fB\-e\fR : [E]rror : max errors allowed by oligonucleotide (0 by default) -.PP +.TP \fB\-h\fR : [H]elp \- print <this> help -.PP +.TP \fB\-i\fR : [I]gnore the given taxonomy id. -.IP Taxonomy id are available using the ecofind program. see its help typing ecofind \fB\-h\fR for more information. -.PP +.TP \fB\-k\fR : [K]ingdom mode : set the kingdom mode -.IP super kingdom mode by default. -.PP +.TP \fB\-l\fR : minimum [L]ength : define the minimum amplication length. -.PP +.TP \fB\-L\fR : maximum [L]ength : define the maximum amplicationlength. -.PP +.TP \fB\-m\fR : Salt correction method for Tm computation (SANTALUCIA : 1 -.IP or OWCZARZY:2, default=1) -.PP +.TP \fB\-r\fR : [R]estricts the search to the given taxonomic id. -.IP Taxonomy id are available using the ecofind program. see its help typing ecofind \fB\-h\fR for more information. -.PP -\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR +.TP first argument : oligonucleotide for direct strand -.PP +.TP second argument : oligonucleotide for reverse strand -.PP -\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR +.TP Table result description : +.TP column 1 : accession number +.TP column 2 : sequence length +.TP column 3 : taxonomic id +.TP column 4 : rank +.TP column 5 : species taxonomic id +.TP column 6 : scientific name +.TP column 7 : genus taxonomic id +.TP column 8 : genus name +.TP column 9 : family taxonomic id +.TP column 10 : family name +.TP column 11 : super kingdom taxonomic id +.TP column 12 : super kingdom name +.TP column 13 : strand (direct or reverse) +.TP column 14 : first oligonucleotide +.TP column 15 : number of errors for the first strand +.TP column 16 : Tm for hybridization of primer 1 at this site +.TP column 17 : second oligonucleotide +.TP column 18 : number of errors for the second strand +.TP column 19 : Tm for hybridization of primer 1 at this site +.TP column 20 : amplification length +.TP column 21 : sequence +.TP column 22 : definition -\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 new file mode 100644 index 0000000..bae4d51 --- /dev/null +++ b/debian/man/ecoisundertaxon.1 @@ -0,0 +1,38 @@ +.\" 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 DESCRIPTION +\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR +.IP +ecoisundertaxon Version 0.1 +.PP +\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR +.IP +synopsis : searching relationship in taxonomy +usage: ecoisundertaxon [options] database +.PP +\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR +.IP +options: +\fB\-1\fR : [FIRST] taxomic id of the hypothetical son +.TP +\fB\-2\fR +: [SECOND] taxonomic id of the hypothetical parent +.TP +\fB\-h\fR +: [H]elp \- print <this> help +.TP +\fB\-v\fR +: [V]erbose mode. Display taxonomic information for both +: taxonomic id. +.PP +\fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR +.IP +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\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\- -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ecopcr.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
