[med-svn] [seer] 02/03: Manual edits fo fix help2man, drop cratemanpages which is in branch manpages
Andreas Tille
tille at debian.org
Thu Mar 23 13:52:40 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 53720f3d8792f9b0395a10cac86cdac3647c2bcf
Author: Andreas Tille <tille at debian.org>
Date: Thu Mar 23 14:31:33 2017 +0100
Manual edits fo fix help2man, drop cratemanpages which is in branch manpages
---
debian/createmanpages | 82 --------------------------------------
debian/mans/R_mds.1 | 34 ++++++++++------
debian/mans/hits_to_fastq.1 | 22 +++++-----
debian/mans/mapping_to_phandango.1 | 22 +++++-----
debian/mans/mash2matrix.1 | 8 +++-
debian/mans/reformat_output.1 | 22 +++++-----
6 files changed, 63 insertions(+), 127 deletions(-)
diff --git a/debian/createmanpages b/debian/createmanpages
deleted file mode 100755
index d215790..0000000
--- a/debian/createmanpages
+++ /dev/null
@@ -1,82 +0,0 @@
-#!/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
index 54e3afe..74086d0 100644
--- a/debian/mans/R_mds.1
+++ b/debian/mans/R_mds.1
@@ -1,4 +1,3 @@
-.\" 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
@@ -8,17 +7,26 @@ R_mds \- project distance matrix into lower number of dimensions
.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 OPTIONS
+.SS Required
+.TP
+\fB\-d\fR, \fB\-\-dist\fR
+Distance matrix output by kmds
+.TP
+\fB\-p\fR, \fB\-\-pheno\fR
+Phenotype file used by seer
+.SS Optional
+.TP
+\fB\-o\fR, \fB\-\-output\fR
+Output prefix (default 'all_structure')
+.TP
+\fB\-\-pc\fR
+Number of dimensions to project into (default 3)
+.TP
+\fB\-R\fR
+R executable (default 'which R')
+.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/hits_to_fastq.1 b/debian/mans/hits_to_fastq.1
index 36b4697..1af9dfc 100644
--- a/debian/mans/hits_to_fastq.1
+++ b/debian/mans/hits_to_fastq.1
@@ -1,4 +1,3 @@
-.\" 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
@@ -7,14 +6,17 @@ hits_to_fastq \- create a fastq for mapping from significant kmers
\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 OPTIONS
+.SS Required
+.TP
+\fB\-k\fR, \fB\-\-kmers\fR
+Significant kmers, as output by seer
+.TP
+\fB\-b\fR, \fB\-\-bonf\fR
+Bonferroni correction to use (try 10e\-8)
+.SS Optional
+.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/mapping_to_phandango.1 b/debian/mans/mapping_to_phandango.1
index ad6506b..4f6d3a5 100644
--- a/debian/mans/mapping_to_phandango.1
+++ b/debian/mans/mapping_to_phandango.1
@@ -1,4 +1,3 @@
-.\" 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
@@ -7,15 +6,18 @@ mapping_to_phandango \- create a plot file for visualisation in 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
+.SH OPTIONS
+.SS Required
+.TP
+\fB\-s\fR, \fB\-\-sam\fR
+Sam file of kmers mapped to reference (unsorted)
+.TP
+\fB\-k\fR, \fB\-\-kmers\fR
+Kmers that were mapped
+.SS Optional
+.TP
+\fB\-m\fR, \fB\-\-map\fR
+Minimum mapping quality
.TP
\fB\-h\fR, \fB\-\-help\fR
Displays this message
diff --git a/debian/mans/mash2matrix.1 b/debian/mans/mash2matrix.1
index 03aa5e4..8672518 100644
--- a/debian/mans/mash2matrix.1
+++ b/debian/mans/mash2matrix.1
@@ -1,4 +1,3 @@
-.\" 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
@@ -11,12 +10,17 @@ between samples.
.PP
NB: the input to mash should be the same order as the .pheno file
generate <assemblies.fa> with:
+.IP
cut \fB\-f\fR 1 metadata.pheno | tr '
+
\&' ' '
.PP
Then run
+.IP
mash sketch \fB\-o\fR reference <assemblies.fa>
+.IP
mash dist reference.msh reference.msh > mash_distances.txt
-\&./mash2matrix.pl mash_distances.txt > all_distances.csv
+.IP
+mash2matrix 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
index 6ee6a98..aa688f5 100644
--- a/debian/mans/reformat_output.1
+++ b/debian/mans/reformat_output.1
@@ -1,4 +1,3 @@
-.\" 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
@@ -7,14 +6,17 @@ reformat_output \- reformats output for easier reading as tsv
\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 OPTIONS
+.SS Required
+.TP
+\fB\-k\fR, \fB\-\-kmers\fR
+Filtered significant kmers, as output by seer + filter_seer
+.TP
+\fB\-p\fR, \fB\-\-pheno\fR
+Phenotype file used by seer
+.SS Optional
+.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.
--
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