[med-svn] [Git][med-team/kmerresistance][master] Add manpage
Andreas Tille
gitlab at salsa.debian.org
Tue Jun 12 09:15:47 BST 2018
Andreas Tille pushed to branch master at Debian Med / kmerresistance
Commits:
ee76cdea by Andreas Tille at 2018-06-12T10:01:16+02:00
Add manpage
- - - - -
5 changed files:
- debian/control
- + debian/createmanpages
- + debian/docs
- + debian/kmerresistance.1
- + debian/manpages
Changes:
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -13,7 +13,7 @@ Package: kmerresistance
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
-Description: correlates mapped genes with the predicted species of WGS samples,
+Description: correlates mapped genes with the predicted species of WGS samples
KmerResistance correlates mapped genes with the predicted species of WGS
samples, where this this allows for identification of genes in samples
which have been poorly sequenced or high accuracy predictions for
=====================================
debian/createmanpages
=====================================
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,32 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//'`
+PROGNAME=`grep "^Package:" debian/control | head -n1 | sed 's/^Package: *//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+
+echo "#!/bin/sh" > /tmp/${progname}
+echo "cat <<EOT" >> /tmp/${progname}
+/usr/bin/${progname} -h | sed 's/^#//' >> /tmp/${progname}
+echo "EOT" >> /tmp/${progname}
+chmod +x /tmp/${progname}
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name="$NAME" \
+ --version-string="$VERSION" /tmp/${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
=====================================
debian/docs
=====================================
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+README*
=====================================
debian/kmerresistance.1
=====================================
--- /dev/null
+++ b/debian/kmerresistance.1
@@ -0,0 +1,127 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
+.TH KMERRESISTANCE "1" "June 2018" "kmerresistance 2.0+git20180205.26467e9" "User Commands"
+.SH NAME
+kmerresistance \- correlates mapped genes with the predicted species of WGS samples
+.SH SYNOPSIS
+
+.SH DESCRIPTION
+KmerResistance correlates mapped genes with the predicted species of WGS
+samples, where this this allows for identification of genes in samples
+which have been poorly sequenced or high accuracy predictions for
+samples with contamination. KmerResistance has one dependency, namely
+KMA to perform the mapping, which is also freely available.
+.SH OPTIONS
+.TP
+\fB\-i\fR
+Input/query file name REQUIRED
+.TP
+\fB\-o\fR
+Output file REQUIRED
+.TP
+\fB\-t_db\fR
+Template DB REQUIRED
+.TP
+\fB\-s_db\fR
+Species DB REQUIRED
+.TP
+\fB\-id\fR
+ID threshhold 70.0
+.TP
+\fB\-dct\fR
+Depth correction threshhold 0.1
+.TP
+\fB\-kma\fR
+alternative KMA kma
+.SS KMA options:
+.TP
+\fB\-i\fR
+Input/query file name None REQUIRED
+.TP
+\fB\-o\fR
+Output file None REQUIRED
+.TP
+\fB\-t_db\fR
+Template DB None REQUIRED
+.TP
+\fB\-k\fR
+Kmersize 16
+.TP
+\fB\-e\fR
+evalue 0.05
+.TP
+\fB\-delta\fR
+Align in pieces of delta 511
+.TP
+\fB\-mem_mode\fR
+Use kmers to choose best
+template, and save memory False
+.TP
+\fB\-ex_mode\fR
+Searh kmers exhaustively False
+.TP
+\fB\-deCon\fR
+Remove contamination False
+.TP
+\fB\-dense\fR
+Do not allow insertions
+in assembly False
+.TP
+\fB\-ref_fsa\fR
+Consensus sequnce will
+have "n" instead of gaps False
+.TP
+\fB\-matrix\fR
+Print assembly matrix False
+.TP
+\fB\-mp\fR
+Minimum phred score 30
+.TP
+\fB\-5p\fR
+Cut a constant number of
+nucleotides from the 5 prime. 0
+.TP
+\fB\-Sparse\fR
+Run KmerFinder False
+.TP
+\fB\-ID\fR
+Minimum ID 1.0%
+.TP
+\fB\-ss\fR
+Sparse sorting (q,c,d) q
+.TP
+\fB\-shm\fR
+Use shared DB made by kma_shm 0 (lvl)
+.TP
+\fB\-swap\fR
+Swap DB to disk 0 (lvl)
+.TP
+\fB\-1t1\fR
+Skip HMM False
+.TP
+\fB\-boot\fR
+Bootstrap sequence False
+.TP
+\fB\-mrs\fR
+Minimum alignment score,
+normalized to alignment length 0.5
+.TP
+\fB\-reward\fR
+Score for match 1
+.TP
+\fB\-penalty\fR
+Penalty for mismatch \fB\-2\fR
+.TP
+\fB\-gapopen\fR
+Penalty for gap opening \fB\-3\fR
+.TP
+\fB\-gapextend\fR
+Penalty for gap extension \fB\-1\fR
+.TP
+\fB\-h\fR
+Shows this help message
+.SH EXAMPLES
+Mapping reads against resistance genes:
+.IP
+ kmerresistance -i sample_1.fastq sample_2.fastq -o out -t_db ResFinder -s_db bacteria
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
=====================================
debian/manpages
=====================================
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
View it on GitLab: https://salsa.debian.org/med-team/kmerresistance/commit/ee76cdeaf0b955a1de9f929bcee1ab132c2892e9
--
View it on GitLab: https://salsa.debian.org/med-team/kmerresistance/commit/ee76cdeaf0b955a1de9f929bcee1ab132c2892e9
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