[med-svn] [bio-tradis] 03/03: Add automatically created manpages
Andreas Tille
tille at debian.org
Sat Mar 4 14:36:33 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 42ce22936d83a1d734369753e51b203bc8203cc8
Author: Andreas Tille <tille at debian.org>
Date: Sat Mar 4 15:26:31 2017 +0100
Add automatically created manpages
---
debian/control | 1 +
debian/createmanpages | 83 ++++++++++++++++++++++++++++++++++
debian/manpages | 1 +
debian/mans/add_tradis_tags.1 | 16 +++++++
debian/mans/bacteria_tradis.1 | 30 ++++++++++++
debian/mans/check_tradis_tags.1 | 13 ++++++
debian/mans/combine_tradis_plots.1 | 28 ++++++++++++
debian/mans/filter_tradis_tags.1 | 16 +++++++
debian/mans/remove_tradis_tags.1 | 16 +++++++
debian/mans/tradis_comparison.1 | 30 ++++++++++++
debian/mans/tradis_essentiality.1 | 21 +++++++++
debian/mans/tradis_gene_insert_sites.1 | 48 ++++++++++++++++++++
debian/mans/tradis_merge_plots.1 | 20 ++++++++
debian/mans/tradis_plot.1 | 15 ++++++
14 files changed, 338 insertions(+)
diff --git a/debian/control b/debian/control
index c3c8865..d34261e 100644
--- a/debian/control
+++ b/debian/control
@@ -22,6 +22,7 @@ Depends: ${perl:Depends},
r-cran-getopt,
r-cran-mass,
libtrycatch-perl
+Suggests: artemis
Description: analyse the output from TraDIS analyses of genomic sequences
Bio-Tradis contains a set of tools to analyse the output from
TraDIS analyses.
diff --git a/debian/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..fdf6baa
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,83 @@
+#!/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 $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=add_tradis_tags
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='Adds transposon sequence and quality tags to the read strings and outputs a BAM' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=bacteria_tradis
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='bio-tradis: run a TraDIS analysis' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=check_tradis_tags
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='bio-tradis: check for the existence of tradis tags in a bam' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=combine_tradis_plots
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='bio-tradis: combine multiple plotfiles and generate updated statistics' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=filter_tradis_tags
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='bio-tradis: filters a BAM file and outputs reads' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=remove_tradis_tags
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='bio-tradis: remove transposon sequence and quality tags from the read strings' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=tradis_comparison
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='bio-tradis: compares two experimental conditions using the method of Dembek et al.' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=tradis_essentiality
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='bio-tradis: produces calls of gene essentiality using an adaptation of the method described in Langridge et al.' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=tradis_gene_insert_sites
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='bio-tradis: take in plot file(s) and an embl file and produce a tab delimited file' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=tradis_merge_plots
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='bio-tradis: Given a study name or ID, group by sample and tag, and generate tab files for input to R' \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=tradis_plot
+help2man --no-info --no-discard-stderr --help-option=" " \
+ --name='bio-tradis: create insertion site plot for Artemis' \
+ --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/manpages b/debian/manpages
new file mode 100644
index 0000000..4f4649b
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*.1
diff --git a/debian/mans/add_tradis_tags.1 b/debian/mans/add_tradis_tags.1
new file mode 100644
index 0000000..0b60122
--- /dev/null
+++ b/debian/mans/add_tradis_tags.1
@@ -0,0 +1,16 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH ADD_TRADIS_TAGS "1" "March 2017" "add_tradis_tags 1.3.1" "User Commands"
+.SH NAME
+add_tradis_tags \- Adds transposon sequence and quality tags to the read strings and outputs a BAM
+.SH SYNOPSIS
+.B add_tags
+\fI\,-b file.bam \/\fR[\fI\,options\/\fR]
+.SH DESCRIPTION
+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
+.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
new file mode 100644
index 0000000..a6b3f60
--- /dev/null
+++ b/debian/mans/bacteria_tradis.1
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH BACTERIA_TRADIS "1" "March 2017" "bacteria_tradis 1.3.1" "User Commands"
+.SH NAME
+bacteria_tradis \- bio-tradis: run a TraDIS analysis
+.SH SYNOPSIS
+.B bacteria_tradis
+[\fI\,options\/\fR]
+.SH DESCRIPTION
+Run a TraDIS analysis. This involves:
+1: filtering the data with tags matching that passed via \fB\-t\fR option
+2: removing the tags from the sequences
+3: mapping
+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
+.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/check_tradis_tags.1 b/debian/mans/check_tradis_tags.1
new file mode 100644
index 0000000..b4b49f8
--- /dev/null
+++ b/debian/mans/check_tradis_tags.1
@@ -0,0 +1,13 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH CHECK_TRADIS_TAGS "1" "March 2017" "check_tradis_tags 1.3.1" "User Commands"
+.SH NAME
+check_tradis_tags \- bio-tradis: check for the existence of tradis tags in a bam
+.SH SYNOPSIS
+.B check_tags
+\fI\,-b file.bam\/\fR
+.SH DESCRIPTION
+Check for the existence of tradis tags in a bam
+.SH OPTIONS
+\fB\-b\fR : bam file with tradis tags
+.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
new file mode 100644
index 0000000..5ee5382
--- /dev/null
+++ b/debian/mans/combine_tradis_plots.1
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH COMBINE_TRADIS_PLOTS "1" "March 2017" "combine_tradis_plots 1.3.1" "User Commands"
+.SH NAME
+combine_tradis_plots \- bio-tradis: combine multiple plotfiles and generate updated statistics
+.SH SYNOPSIS
+.B combine_tradis_plots
+\fI\,-p plots.txt\/\fR
+.SH DESCRIPTION
+Combine multiple plotfiles and generate updated statistics for the combined
+files. Takes a tab\-delimited file with an ID as the first column followed by
+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
+tradis1 plot1.1.gz plot1.2.gz plot1.3.gz
+tradis2 plot2.1.gz plot2.2.gz
+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,
+tradis2.insertion_site_plot.gz, tradis3.insertion_site_plot.gz
+2. 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)
+.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
new file mode 100644
index 0000000..e4253d4
--- /dev/null
+++ b/debian/mans/filter_tradis_tags.1
@@ -0,0 +1,16 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH FILTER_TRADIS_TAGS "1" "March 2017" "filter_tradis_tags 1.3.1" "User Commands"
+.SH NAME
+filter_tradis_tags \- bio-tradis: filters a BAM file and outputs reads
+.SH SYNOPSIS
+.B filter_tags
+\fI\,-b file.bam -t tag \/\fR[\fI\,options\/\fR]
+.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)
+.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
new file mode 100644
index 0000000..f251359
--- /dev/null
+++ b/debian/mans/remove_tradis_tags.1
@@ -0,0 +1,16 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH REMOVE_TRADIS_TAGS "1" "March 2017" "remove_tradis_tags 1.3.1" "User Commands"
+.SH NAME
+remove_tradis_tags \- bio-tradis: remove transposon sequence and quality tags from the read strings
+.SH SYNOPSIS
+.B remove_tags
+\fI\,-f file.fastq \/\fR[\fI\,options\/\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)
+.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
new file mode 100644
index 0000000..7fd5933
--- /dev/null
+++ b/debian/mans/tradis_comparison.1
@@ -0,0 +1,30 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH TRADIS_COMPARISON "1" "March 2017" "tradis_comparison 1.3.1" "User Commands"
+.SH NAME
+tradis_comparison \- bio-tradis: compares two experimental conditions using the method of Dembek et al.
+.SH SYNOPSIS
+.B tradis_comparison.R
+[\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
+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
+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
new file mode 100644
index 0000000..cf5a86a
--- /dev/null
+++ b/debian/mans/tradis_essentiality.1
@@ -0,0 +1,21 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH TRADIS_ESSENTIALITY "1" "March 2017" "tradis_essentiality 1.3.1" "User Commands"
+.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
+\fI\,data.tab\/\fR
+.SH DESCRIPTION
+Produces calls of gene essentiality using an adaptation of the method
+described in Langridge et al. Genome Research 2009 and Barquist et al.
+NAR 2013. A loess curve is fit to the distribution of insertion
+indices, and used to identify the minima between the 'essential' and
+\&'non\-essential' distributions. These distributions are then used to fit
+gamma distributions, which are then used to calculate log\-odds ratios,
+which are used to determine an insertion\-index threshold for gene
+essentiality. Note that this analysis requires a saturated mutant
+library, and is not suitable for the analysis of data sets with low
+insertion density. The script produces a number of diagnostic plots
+which can be used to verify that this condition has been met.
+.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_gene_insert_sites.1 b/debian/mans/tradis_gene_insert_sites.1
new file mode 100644
index 0000000..c0ad7ab
--- /dev/null
+++ b/debian/mans/tradis_gene_insert_sites.1
@@ -0,0 +1,48 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH TRADIS_GENE_INSERT_SITES "1" "March 2017" "tradis_gene_insert_sites 1.3.1" "User Commands"
+.SH NAME
+tradis_gene_insert_sites \- bio-tradis: take in plot file(s) and an embl file and produce a tab delimited file
+.SH SYNOPSIS
+.B tradis_gene_insert_sites
+
+.SH DESCRIPTION
+Take in a plot file(s) and an embl file and produce a tab delimited file with insert site details to use as input to an R script to t
+est for essentiality.
+.TP
+\fB\-o\fR|output_suffix
+<suffix to add to output files (optional, default = tradis_gene_insert_sites.csv)>
+.TP
+\fB\-trim5\fR
+<trim insertion sites from 5' end of gene (optional, default = 0)>
+.TP
+\fB\-trim3\fR
+<trim insertion sites from 3' end of gene (optional, default = 0)>
+.TP
+\fB\-j\fR|joined_output
+<output a single file with all info. default = one file per input file>
+.TP
+\fB\-h\fR|help
+<display this message>
+.PP
+tradis_gene_insert_sites my_annotation.embl my_insert_site_plot.gz
+.PP
+tradis_gene_insert_sites my_annotation.embl my_insert_site_plot
+.PP
+# 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
+tradis_gene_insert_sites \fB\-o\fR my_output.csv my_annotation.embl my_insert_site_plot1
+.PP
+# 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
+# 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
+Resulting file: joined_output.output_suffix.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/tradis_merge_plots.1 b/debian/mans/tradis_merge_plots.1
new file mode 100644
index 0000000..751004a
--- /dev/null
+++ b/debian/mans/tradis_merge_plots.1
@@ -0,0 +1,20 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH TRADIS_MERGE_PLOTS "1" "March 2017" "tradis_merge_plots 1.3.1" "User Commands"
+.SH NAME
+tradis_merge_plots \- bio-tradis: Given a study name or ID, group by sample and tag, and generate tab files for input to R
+.SH SYNOPSIS
+.B tradis_merge_plots
+[\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
+# run over sequencescape study 1234
+tradis_merge_plots 1234
+.PP
+# Provide a name instead of a study ID
+tradis_merge_plots "My Study"
+.PP
+# This help message
+tradis_merge_plots \fB\-h\fR
+.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_plot.1 b/debian/mans/tradis_plot.1
new file mode 100644
index 0000000..8282005
--- /dev/null
+++ b/debian/mans/tradis_plot.1
@@ -0,0 +1,15 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.4.
+.TH TRADIS_PLOT "1" "March 2017" "tradis_plot 1.3.1" "User Commands"
+.SH NAME
+tradis_plot \- bio-tradis: create insertion site plot for Artemis
+.SH SYNOPSIS
+.B tradis_plot
+\fI\,-f file.bam \/\fR[\fI\,options\/\fR]
+.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)
+.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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