[med-svn] [Git][med-team/kma][master] Add autogenerated manpages
Andreas Tille
gitlab at salsa.debian.org
Sat Oct 27 07:00:53 BST 2018
Andreas Tille pushed to branch master at Debian Med / kma
Commits:
b58f9042 by Andreas Tille at 2018-06-12T15:15:20Z
Add autogenerated manpages
- - - - -
5 changed files:
- + debian/createmanpages
- + debian/kma.1
- + debian/kma_index.1
- + debian/kma_shm.1
- + debian/manpages
Changes:
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,34 @@
+#!/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 $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+for progname in kma kma_index kma_shm ; do
+ NAME=`${progname} -h | head -n1 | sed -e 's/^# \+[^ ]\+ \+//' -e 's/\. *$//'`
+
+ echo "#!/bin/sh" > /tmp/${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
+done
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
=====================================
debian/kma.1
=====================================
@@ -0,0 +1,141 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
+.TH KMA "1" "June 2018" "kma 0.14.4+git20180611.7e14ef6" "User Commands"
+.SH NAME
+kma \- mapps raw reads to a template database, for optimal performance it is designed to use 3 threads
+.SH DESCRIPTION
+.IP
+KMA\-0.14.4 mapps raw reads to a template database, for optimal performance it is designed to use 3 threads.
+Options are: Desc: Default: Requirements:
+.TP
+\fB\-o\fR
+Output file None REQUIRED
+.TP
+\fB\-t_db\fR
+Template DB None REQUIRED
+.TP
+\fB\-i\fR
+Input file name(s) STDIN
+.TP
+\fB\-ipe\fR
+Input paired end file name(s)
+.TP
+\fB\-int\fR
+Input interleaved file name(s)
+.TP
+\fB\-k\fR
+Kmersize DB defined
+.TP
+\fB\-e\fR
+evalue 0.05
+.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\-a\fR
+Print all best mappings 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
+Only count kmers False
+.TP
+\fB\-Mt1\fR
+Map only to "num" template. 0 / False
+.TP
+\fB\-ID\fR
+Minimum ID 1.0%
+.TP
+\fB\-ss\fR
+Sparse sorting (q,c,d) q
+.TP
+\fB\-pm\fR
+Pairing method (p,u,f) u
+.TP
+\fB\-fpm\fR
+Fine Pairing method (p,u,f) u
+.TP
+\fB\-apm\fR
+Sets both pm and fpm u
+.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\-bc\fR
+Base calls should be
+significantly overrepresented. True
+.TP
+\fB\-bc90\fR
+Base calls should be both
+significantly overrepresented,
+and have 90% agreement. False
+.TP
+\fB\-bcNano\fR
+Call bases at suspicious
+deletions, made for nanopore. False
+.TP
+\fB\-and\fR
+Both mrs and p_value thresholds
+has to reached to in order to
+report a template hit. or
+.TP
+\fB\-mrs\fR
+Minimum alignment score,
+normalized to alignment length 0.50
+.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\-per\fR
+Reward for pairing reads 7
+.TP
+\fB\-t\fR
+Number of threads 1
+.TP
+\fB\-v\fR
+Version
+.TP
+\fB\-h\fR
+Shows this help message
+.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/kma_index.1
=====================================
@@ -0,0 +1,62 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
+.TH KMA_INDEX "1" "June 2018" "kma_index 0.14.4+git20180611.7e14ef6" "User Commands"
+.SH NAME
+kma_index \- creates the databases needed to run KMA, from a list of fasta files given
+.SH DESCRIPTION
+.IP
+kma_index creates the databases needed to run KMA, from a list of fasta files given.
+Options are: Desc: Default:
+.TP
+\fB\-i\fR
+Input/query file name (STDIN: "\-\-") None
+.TP
+\fB\-o\fR
+Output file Input/template file
+.TP
+\fB\-batch\fR
+Batch input file
+.TP
+\fB\-deCon\fR
+File with contamination (STDIN: "\-\-") None/False
+.TP
+\fB\-batchD\fR
+Batch decon file
+.TP
+\fB\-t_db\fR
+Add to existing DB None/False
+.TP
+\fB\-k\fR
+Kmersize 16
+.TP
+\fB\-k_t\fR
+Kmersize for template identification 16
+.TP
+\fB\-k_i\fR
+Kmersize for indexing 16
+.TP
+\fB\-ML\fR
+Minimum length of templates kmersize (16)
+.TP
+\fB\-CS\fR
+Start Chain size 1 M
+.TP
+\fB\-ME\fR
+Mega DB False
+.TP
+\fB\-Sparse\fR
+Make Sparse DB ('\-' for no prefix) None/False
+.TP
+\fB\-ht\fR
+Homology template 1.0
+.TP
+\fB\-hq\fR
+Homology query 1.0
+.TP
+\fB\-and\fR
+Both homolgy thresholds
+has to be reached or
+.TP
+\fB\-h\fR
+Shows this help message
+.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/kma_shm.1
=====================================
@@ -0,0 +1,25 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.6.
+.TH KMA_SHM "1" "June 2018" "kma_shm 0.14.4+git20180611.7e14ef6" "User Commands"
+.SH NAME
+kma_shm \- sets up a shared database (sysV) for mapping with KMA
+.SH DESCRIPTION
+.IP
+kma_shm sets up a shared database (sysV) for mapping with KMA.
+Options are: Desc: Default: Requirements:
+.TP
+\fB\-t_db\fR
+Template DB None REQUIRED
+.TP
+\fB\-destroy\fR
+Destroy shared DB False
+.TP
+\fB\-shmLvl\fR
+Level of shared memory 1
+.TP
+\fB\-shm\-h\fR
+Explain shm levels
+.TP
+\fB\-h\fR
+Shows this help message
+.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
=====================================
@@ -0,0 +1 @@
+debian/*.1
View it on GitLab: https://salsa.debian.org/med-team/kma/commit/b58f9042625f288adc2415a3a9454c748bc258d4
--
View it on GitLab: https://salsa.debian.org/med-team/kma/commit/b58f9042625f288adc2415a3a9454c748bc258d4
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