[med-svn] [bio-tradis] 01/01: Manually enhanced manpages
Andreas Tille
tille at debian.org
Sat Mar 4 17:34:21 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bio-tradis.
commit 862c8c656cc37e1ea8ef2dc4b27996431e8c81b2
Author: Andreas Tille <tille at debian.org>
Date: Sat Mar 4 18:27:23 2017 +0100
Manually enhanced manpages
---
debian/mans/add_tradis_tags.1 | 12 ++++++--
debian/mans/bacteria_tradis.1 | 52 +++++++++++++++++++++++++---------
debian/mans/combine_tradis_plots.1 | 19 +++++++++----
debian/mans/filter_tradis_tags.1 | 16 ++++++++---
debian/mans/remove_tradis_tags.1 | 16 ++++++++---
debian/mans/tradis_comparison.1 | 38 ++++++++++++++-----------
debian/mans/tradis_essentiality.1 | 2 +-
debian/mans/tradis_gene_insert_sites.1 | 18 ++++++------
debian/mans/tradis_merge_plots.1 | 7 +++--
debian/mans/tradis_plot.1 | 12 ++++++--
10 files changed, 131 insertions(+), 61 deletions(-)
diff --git a/debian/mans/add_tradis_tags.1 b/debian/mans/add_tradis_tags.1
index 0b60122..cc78ee1 100644
--- a/debian/mans/add_tradis_tags.1
+++ b/debian/mans/add_tradis_tags.1
@@ -9,8 +9,14 @@ add_tradis_tags \- Adds transposon sequence and quality tags to the read strings
Adds transposon sequence and quality tags to the read strings and
outputs a BAM.
.SH OPTIONS
-\fB\-b\fR : bam file with tradis tags
-\fB\-o\fR : output BAM name (optional. default: <file>.tr.bam)
-\fB\-v\fR : verbose debugging output
+.TP
+\fB\-b\fR
+bam file with tradis tags
+.TP
+\fB\-o\fR
+output BAM name (optional. default: <file>.tr.bam)
+.TP
+\fB\-v\fR
+verbose debugging output
.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/bacteria_tradis.1 b/debian/mans/bacteria_tradis.1
index a6b3f60..4dee9c7 100644
--- a/debian/mans/bacteria_tradis.1
+++ b/debian/mans/bacteria_tradis.1
@@ -13,18 +13,44 @@ Run a TraDIS analysis. This involves:
4: creating an insertion site plot
5: creating a stats summary
.SH OPTIONS
-\fB\-f\fR : text file listing fastq files with tradis tags attached
-\fB\-t\fR : tag to search for
-\fB\-r\fR : reference genome in fasta format (.fa)
-\fB\-td\fR : tag direction \- 3 or 5 (optional. default = 3)
-\fB\-mm\fR : number of mismatches allowed when matching tag (optional. default = 0)
-\fB\-m\fR : mapping quality cutoff score (optional. default = 30)
-\fB\-\-smalt_k\fR : custom k\-mer value for SMALT mapping (optional)
-\fB\-\-smalt_s\fR : custom step size for SMALT mapping (optional)
-\fB\-\-smalt_y\fR : custom y parameter for SMALT (optional. default = 0.96)
-\fB\-\-smalt_r\fR : custom r parameter for SMALT (optional. default = \fB\-1\fR)
-\fB\-n\fR : number of threads to use for SMALT and samtools sort (optional. default = 1)
-\fB\-e\fR : set defaults for essentiality experiment (smalt_r = 0, \fB\-m\fR = 0)
-\fB\-v\fR : verbose debugging output
+.TP
+\fB\-f\fR
+text file listing fastq files with tradis tags attached
+.TP
+\fB\-t\fR
+tag to search for
+.TP
+\fB\-r\fR
+reference genome in fasta format (.fa)
+.TP
+\fB\-td\fR
+tag direction \- 3 or 5 (optional. default = 3)
+.TP
+\fB\-mm\fR
+number of mismatches allowed when matching tag (optional. default = 0)
+.TP
+\fB\-m\fR
+mapping quality cutoff score (optional. default = 30)
+.TP
+\fB\-\-smalt_k\fR
+custom k\-mer value for SMALT mapping (optional)
+.TP
+\fB\-\-smalt_s\fR
+custom step size for SMALT mapping (optional)
+.TP
+\fB\-\-smalt_y\fR
+custom y parameter for SMALT (optional. default = 0.96)
+.TP
+\fB\-\-smalt_r\fR
+custom r parameter for SMALT (optional. default = \fB\-1\fR)
+.TP
+\fB\-n\fR
+number of threads to use for SMALT and samtools sort (optional. default = 1)
+.TP
+\fB\-e\fR
+set defaults for essentiality experiment (smalt_r = 0, \fB\-m\fR = 0)
+.TP
+\fB\-v\fR
+verbose debugging output
.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/combine_tradis_plots.1 b/debian/mans/combine_tradis_plots.1
index 5ee5382..c49a2d7 100644
--- a/debian/mans/combine_tradis_plots.1
+++ b/debian/mans/combine_tradis_plots.1
@@ -12,17 +12,26 @@ a list of plotfiles to combine per row. The ID will be used to name the new
plotfile and as an identifier in the stats file, so ensure these are unique.
.PP
For example, an input file named plots_to_combine.txt:
-.PP
+.IP
tradis1 plot1.1.gz plot1.2.gz plot1.3.gz
+.IP
tradis2 plot2.1.gz plot2.2.gz
+.IP
tradis3 plot3.1.gz plot3.2.gz plot3.3.gz plot3.4.gz
.PP
will produce
-1. a directory named combined with 3 files \- tradis1.insertion_site_plot.gz,
+.nr step 1 1
+.IP \n[step] 2
+a directory named combined with 3 files \- tradis1.insertion_site_plot.gz,
tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz
-2. a stats file named plots_to_combine.stats
+.IP \n+[step]
+a stats file named plots_to_combine.stats
.SH OPTIONS
-\fB\-p\fR|plotfile : file with plots to be combined
-\fB\-o\fR|output_dir : name of directory for output (default: combined)
+.TP
+\fB\-p\fR|plotfile
+file with plots to be combined
+.TP
+\fB\-o\fR|output_dir
+name of directory for output (default: combined)
.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/filter_tradis_tags.1 b/debian/mans/filter_tradis_tags.1
index e4253d4..a41ee1d 100644
--- a/debian/mans/filter_tradis_tags.1
+++ b/debian/mans/filter_tradis_tags.1
@@ -8,9 +8,17 @@ filter_tradis_tags \- bio-tradis: filters a BAM file and outputs reads
.SH DESCRIPTION
Filters a BAM file and outputs reads with tag matching \fB\-t\fR option
.SH OPTIONS
-\fB\-f\fR : fastq file with tradis tags attached
-\fB\-t\fR : tag to search for
-\fB\-m\fR : number of mismatches to allow when matching tag (optional. default = 0)
-\fB\-o\fR : output file name (optional. default: <file>.tag.fastq)
+.TP
+\fB\-f\fR
+fastq file with tradis tags attached
+.TP
+\fB\-t\fR
+tag to search for
+.TP
+\fB\-m\fR
+number of mismatches to allow when matching tag (optional. default = 0)
+.TP
+\fB\-o\fR
+output file name (optional. default: <file>.tag.fastq)
.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/remove_tradis_tags.1 b/debian/mans/remove_tradis_tags.1
index f251359..f4dace5 100644
--- a/debian/mans/remove_tradis_tags.1
+++ b/debian/mans/remove_tradis_tags.1
@@ -8,9 +8,17 @@ remove_tradis_tags \- bio-tradis: remove transposon sequence and quality tags fr
.SH DESCRIPTION
Removes transposon sequence and quality tags from the read strings
.SH OPTIONS
-\fB\-f\fR : fastq file with tradis tags
-\fB\-t\fR : tag to remove
-\fB\-m\fR : number of mismatches to allow when matching tag (optional. default = 0)
-\fB\-o\fR : output file name (optional. default: <file>.rmtag.fastq)
+.TP
+\fB\-f\fR
+fastq file with tradis tags
+.TP
+\fB\-t\fR
+tag to remove
+.TP
+\fB\-m\fR
+number of mismatches to allow when matching tag (optional. default = 0)
+.TP
+\fB\-o\fR
+output file name (optional. default: <file>.rmtag.fastq)
.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/tradis_comparison.1 b/debian/mans/tradis_comparison.1
index 7fd5933..b6e0c1f 100644
--- a/debian/mans/tradis_comparison.1
+++ b/debian/mans/tradis_comparison.1
@@ -3,28 +3,34 @@
.SH NAME
tradis_comparison \- bio-tradis: compares two experimental conditions using the method of Dembek et al.
.SH SYNOPSIS
-.B tradis_comparison.R
+.B tradis_comparison
[\fI\,-h\/\fR] [\fI\,-f\/\fR] [\fI\,-t read cutoff\/\fR] [\fI\,-o outputfile.csv\/\fR] [\fI\,-p outputplot.pdf\/\fR] \fI\,--controls controls.txt --conditions conditions.txt\/\fR
.SH DESCRIPTION
-Loading required package: limma
-.PP
Compares two experimental conditions using the method of Dembek et al.
mBio 2015. Read counts per gene are compared using edgeR. This analysis
requires experimental replicates.
-.PP
-Required Arguments:
-.PP
-\fB\-\-controls\fR : 'control' libraries, generally growth in a permissive
-condition
-\fB\-\-conditions\fR : libraries exposed to the experimental condition being
+.SH OPTIONS
+.SS Required Arguments:
+.TP
+\fB\-\-controls\fR
+control libraries, generally growth in a permissive condition
+.TP
+\fB\-\-conditions\fR
+libraries exposed to the experimental condition being
compared
-.PP
-Optional Arguments:
-.PP
-\fB\-o\fR : output filename
-\fB\-p\fR : output filename for diagnostic plots
-\fB\-f\fR : enable filtering on minimum read counts
-\fB\-t\fR : if \fB\-\-filter\fR is enabled, sets minimum read count necessary in one
+.SS Optional Arguments:
+.TP
+\fB\-o\fR
+output filename
+.TP
+\fB\-p\fR
+output filename for diagnostic plots
+.TP
+\fB\-f\fR
+enable filtering on minimum read counts
+.TP
+\fB\-t\fR
+if \fB\-\-filter\fR is enabled, sets minimum read count necessary in one
condition for a gene to be included in the comparison.
.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/tradis_essentiality.1 b/debian/mans/tradis_essentiality.1
index cf5a86a..2385f82 100644
--- a/debian/mans/tradis_essentiality.1
+++ b/debian/mans/tradis_essentiality.1
@@ -3,7 +3,7 @@
.SH NAME
tradis_essentiality \- bio-tradis: produces calls of gene essentiality using an adaptation of the method described in Langridge et al.
.SH SYNOPSIS
-.B tradis_essentiality.R
+.B tradis_essentiality
\fI\,data.tab\/\fR
.SH DESCRIPTION
Produces calls of gene essentiality using an adaptation of the method
diff --git a/debian/mans/tradis_gene_insert_sites.1 b/debian/mans/tradis_gene_insert_sites.1
index c0ad7ab..c2b70c6 100644
--- a/debian/mans/tradis_gene_insert_sites.1
+++ b/debian/mans/tradis_gene_insert_sites.1
@@ -22,24 +22,24 @@ est for essentiality.
<output a single file with all info. default = one file per input file>
.TP
\fB\-h\fR|help
-<display this message>
-.PP
+display this message
+.SH EXAMPLES
+.IP
tradis_gene_insert_sites my_annotation.embl my_insert_site_plot.gz
-.PP
+.IP
tradis_gene_insert_sites my_annotation.embl my_insert_site_plot
-.PP
+.TP
# multiple plot files
tradis_gene_insert_sites my_annotation.embl plot1.gz plot2.gz plot3.gz plot4.gz
-.PP
-# specifiy an output suffix
-# this will result in a file named my_insert_site_plot1.my_output.csv
+.TP
+# specify an output suffix this will result in a file named my_insert_site_plot1.my_output.csv
tradis_gene_insert_sites \fB\-o\fR my_output.csv my_annotation.embl my_insert_site_plot1
-.PP
+.TP
# Trim insertion sites from start or end of gene
tradis_gene_insert_sites my_annotation.embl \fB\-trim5\fR 0.1 \fB\-trim3\fR 0.1 my_annotation.embl my_insert_site_plot.gz
.PP
The trim parameter is the fraction of the gene length trimmed.
-.PP
+.TP
# place all info into a single file
tradis_gene_insert_sites \fB\-o\fR output_suffix.csv \fB\-j\fR my_annotation.embl plot1.gz plot2.gz plot3.gz
.PP
diff --git a/debian/mans/tradis_merge_plots.1 b/debian/mans/tradis_merge_plots.1
index 751004a..d736496 100644
--- a/debian/mans/tradis_merge_plots.1
+++ b/debian/mans/tradis_merge_plots.1
@@ -7,13 +7,14 @@ tradis_merge_plots \- bio-tradis: Given a study name or ID, group by sample and
[\fI\,options\/\fR]
.SH DESCRIPTION
Given a study name or ID, group by sample and tag, and generate tab files for input to R.
-.PP
+.SH EXAMPLES
+.TP
# run over sequencescape study 1234
tradis_merge_plots 1234
-.PP
+.TP
# Provide a name instead of a study ID
tradis_merge_plots "My Study"
-.PP
+.TP
# This help message
tradis_merge_plots \fB\-h\fR
.SH AUTHOR
diff --git a/debian/mans/tradis_plot.1 b/debian/mans/tradis_plot.1
index 8282005..f52ea91 100644
--- a/debian/mans/tradis_plot.1
+++ b/debian/mans/tradis_plot.1
@@ -8,8 +8,14 @@ tradis_plot \- bio-tradis: create insertion site plot for Artemis
.SH DESCRIPTION
Create insertion site plot for Artemis
.SH OPTIONS
-\fB\-f\fR : mapped, sorted bam file
-\fB\-m\fR : mapping quality must be greater than X (optional. default: 30)
-\fB\-o\fR : output base name for plot (optional. default: tradis.plot)
+.TP
+\fB\-f\fR
+mapped, sorted bam file
+.TP
+\fB\-m\fR
+mapping quality must be greater than X (optional. default: 30)
+.TP
+\fB\-o\fR
+output base name for plot (optional. default: tradis.plot)
.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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