[med-svn] [seer] 03/03: Autogenerate manpages - needs manual editing
Andreas Tille
tille at debian.org
Thu Mar 23 13:13:40 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository seer.
commit e4b83f07ffbbd8d01040e2bccba1457f53a3abe0
Author: Andreas Tille <tille at debian.org>
Date: Thu Mar 23 14:13:17 2017 +0100
Autogenerate manpages - needs manual editing
---
debian/createmanpages | 82 ++++++++++++++++++++++++++++++++++++++
debian/mans/R_mds.1 | 24 +++++++++++
debian/mans/hits_to_fastq.1 | 20 ++++++++++
debian/mans/mapping_to_phandango.1 | 23 +++++++++++
debian/mans/mash2matrix.1 | 22 ++++++++++
debian/mans/reformat_output.1 | 20 ++++++++++
6 files changed, 191 insertions(+)
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..d215790
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,82 @@
+#!/bin/sh
+MANDIR=debian/mans
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=blast_top_hits
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='reduces a blast or blat output file to the top hit for each query sequence only' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=combineKmers
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='basic algorithm to combine kmer counts across samples' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=filter_seer
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='post filtering of significant kmers' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=kmds
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='control for population structure' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=map_back
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='context of significant kmers' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=seer
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='sequence element enrichment analysis' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=R_mds
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='project distance matrix into lower number of dimensions' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=hits_to_fastq
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='create a fastq for mapping from significant kmers' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=mapping_to_phandango
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='create a plot file for visualisation in phandango' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=mash2matrix
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='create all pairwise distances between samples' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=reformat_output
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name='reformats output for easier reading as tsv' \
+ --version-string="$VERSION" ${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
+
diff --git a/debian/mans/R_mds.1 b/debian/mans/R_mds.1
new file mode 100644
index 0000000..54e3afe
--- /dev/null
+++ b/debian/mans/R_mds.1
@@ -0,0 +1,24 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH R_MDS "1" "March 2017" "R_mds 1.1.2" "User Commands"
+.SH NAME
+R_mds \- project distance matrix into lower number of dimensions
+.SH SYNOPSIS
+.B R_mds
+\fI\,-k <filtered_kmers.txt> -p <pheno_file>\/\fR
+.SH DESCRIPTION
+Projects distance matrix into lower number of dimensions
+Requires R and rhdf5 to be installed, see github wiki for more details
+.IP
+Options
+.IP
+Required
+\fB\-d\fR, \fB\-\-dist\fR Distance matrix output by kmds
+\fB\-p\fR, \fB\-\-pheno\fR Phenotype file used by seer
+.IP
+Optional
+\fB\-o\fR, \fB\-\-output\fR Output prefix (default 'all_structure')
+\fB\-\-pc\fR Number of dimensions to project into (default 3)
+\fB\-R\fR R executable (default 'which R')
+\fB\-h\fR, \fB\-\-help\fR Displays this 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.
diff --git a/debian/mans/hits_to_fastq.1 b/debian/mans/hits_to_fastq.1
new file mode 100644
index 0000000..36b4697
--- /dev/null
+++ b/debian/mans/hits_to_fastq.1
@@ -0,0 +1,20 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH HITS_TO_FASTQ "1" "March 2017" "hits_to_fastq 1.1.2" "User Commands"
+.SH NAME
+hits_to_fastq \- create a fastq for mapping from significant kmers
+.SH SYNOPSIS
+.B hits_to_fastq
+\fI\,-k <significant_kmers.txt> -b <bonferroni_correction>\/\fR
+.SH DESCRIPTION
+Creates a fastq for mapping from significant kmers
+.IP
+Options
+.IP
+Required
+\fB\-k\fR, \fB\-\-kmers\fR Significant kmers, as output by seer
+\fB\-b\fR, \fB\-\-bonf\fR Bonferroni correction to use (try 10e\-8)
+.IP
+Optional
+\fB\-h\fR, \fB\-\-help\fR Displays this 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.
diff --git a/debian/mans/mapping_to_phandango.1 b/debian/mans/mapping_to_phandango.1
new file mode 100644
index 0000000..ad6506b
--- /dev/null
+++ b/debian/mans/mapping_to_phandango.1
@@ -0,0 +1,23 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH MAPPING_TO_PHANDANGO "1" "March 2017" "mapping_to_phandango 1.1.2" "User Commands"
+.SH NAME
+mapping_to_phandango \- create a plot file for visualisation in phandango
+.SH SYNOPSIS
+.B mapping_to_phandango
+\fI\,-s <sam_file> -k <seer_kmers> > phandango.plot\/\fR
+.SH DESCRIPTION
+Creates a plot file for visualisation in phandango
+.IP
+Options
+.IP
+Required
+\fB\-s\fR, \fB\-\-sam\fR Sam file of kmers mapped to reference (unsorted)
+\fB\-k\fR, \fB\-\-kmers\fR Kmers that were mapped
+.IP
+Optional
+\fB\-m\fR, \fB\-\-map\fR Minimum mapping quality
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+Displays this 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.
diff --git a/debian/mans/mash2matrix.1 b/debian/mans/mash2matrix.1
new file mode 100644
index 0000000..03aa5e4
--- /dev/null
+++ b/debian/mans/mash2matrix.1
@@ -0,0 +1,22 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH MASH2MATRIX "1" "March 2017" "mash2matrix 1.1.2" "User Commands"
+.SH NAME
+mash2matrix \- create all pairwise distances between samples
+.SH SYNOPSIS
+.B mash2matrix
+\fI\,<matrix_in> > all_distances.csv\/\fR
+.SH DESCRIPTION
+Uses mash (http://mash.readthedocs.io/) to create all pairwise distances
+between samples.
+.PP
+NB: the input to mash should be the same order as the .pheno file
+generate <assemblies.fa> with:
+cut \fB\-f\fR 1 metadata.pheno | tr '
+\&' ' '
+.PP
+Then run
+mash sketch \fB\-o\fR reference <assemblies.fa>
+mash dist reference.msh reference.msh > mash_distances.txt
+\&./mash2matrix.pl mash_distances.txt > all_distances.csv
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/mans/reformat_output.1 b/debian/mans/reformat_output.1
new file mode 100644
index 0000000..6ee6a98
--- /dev/null
+++ b/debian/mans/reformat_output.1
@@ -0,0 +1,20 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH REFORMAT_OUTPUT "1" "March 2017" "reformat_output 1.1.2" "User Commands"
+.SH NAME
+reformat_output \- reformats output for easier reading as tsv
+.SH SYNOPSIS
+.B hits_to_matrix.pl
+\fI\,-k <filtered_kmers.txt> -p <pheno_file>\/\fR
+.SH DESCRIPTION
+Reformats output for easier reading as tsv. Prints to stdout
+.IP
+Options
+.IP
+Required
+\fB\-k\fR, \fB\-\-kmers\fR Filtered significant kmers, as output by seer + filter_seer
+\fB\-p\fR, \fB\-\-pheno\fR Phenotype file used by seer
+.IP
+Optional
+\fB\-h\fR, \fB\-\-help\fR Displays this 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.
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seer.git
More information about the debian-med-commit
mailing list