[med-svn] [manta] 01/06: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository manta.

commit 8a403c31aacabb4db85d5d94bc34006a2f682362
Author: Andreas Tille <tille at debian.org>
Date:   Tue May 2 13:42:45 2017 +0200

    Add manpage
---
 debian/configManta.1  | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/createmanpages | 22 ++++++++++++++
 debian/manpages       |  1 +
 3 files changed, 103 insertions(+)

diff --git a/debian/configManta.1 b/debian/configManta.1
new file mode 100644
index 0000000..ca9d119
--- /dev/null
+++ b/debian/configManta.1
@@ -0,0 +1,80 @@
+.TH CONFIGMANTA "1" "May 2017" "configManta 1.0.2" "User Commands"
+.SH NAME
+configManta \- configure the Manta SV analysis pipeline
+.SH SYNOPSIS
+.B configManta.py
+[\fI\,options\/\fR]
+.SH DESCRIPTION
+This script configures the Manta SV analysis pipeline.
+You must specify a BAM or CRAM file for at least one sample.
+.PP
+Configuration will produce a workflow run script which
+can execute the workflow on a single node or through
+sge and resume any interrupted execution.
+.SH OPTIONS
+.TP
+\fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-config\fR=\fI\,FILE\/\fR
+provide a configuration file to override defaults in
+global config file
+(\fI\,/usr/share/manta/configManta.py.ini\/\fP)
+.TP
+\fB\-\-allHelp\fR
+show all extended/hidden options
+.IP
+.SS Workflow options
+.TP
+\fB\-\-bam\fR=\fI\,FILE\/\fR, \fB\-\-normalBam\fR=\fI\,FILE\/\fR
+Normal sample BAM or CRAM file. May be specified more
+than once, multiple inputs will be treated as each BAM
+file representing a different sample. [optional] (no
+default)
+.TP
+\fB\-\-tumorBam\fR=\fI\,FILE\/\fR, \fB\-\-tumourBam\fR=\fI\,FILE\/\fR
+Tumor sample BAM or CRAM file. Only up to one tumor
+bam file accepted. [optional] (no default)
+.TP
+\fB\-\-exome\fR
+Set options for WES input: turn off depth filters
+.TP
+\fB\-\-rna\fR
+Set options for RNA\-Seq input: turn off depth filters
+and don't treat anomalous reads as SV evidence when
+the proper\-pair bit is set.
+.TP
+\fB\-\-unstrandedRNA\fR
+Set if RNA\-Seq input is unstranded: Allows splicejunctions on either strand
+.TP
+\fB\-\-referenceFasta\fR=\fI\,FILE\/\fR
+samtools\-indexed reference fasta file [required]
+.TP
+\fB\-\-runDir\fR=\fI\,DIR\/\fR
+Run script and run output will be written to this
+directory [required] (default: MantaWorkflow)
+.SS Extended options:
+.PP
+These options are either unlikely to be reset after initial site
+configuration or only of interest for workflow development/debugging.
+They will not be printed here if a default exists unless \fB\-\-allHelp\fR is
+specified
+.TP
+\fB\-\-scanSizeMb\fR=\fI\,INT\/\fR
+Maximum sequence region size (in megabases) scanned by
+each task during SV Locus graph generation. (default:
+12)
+.TP
+\fB\-\-region\fR=\fI\,REGION\/\fR
+Limit the analysis to a region of the genome for
+debugging purposes. If this argument is provided
+multiple times all specified regions will be analyzed
+together. All regions must be non\-overlapping to get a
+meaningful result. Examples: '\-\-region chr20' (whole
+chromosome), '\-\-region chr2:100\-2000 \fB\-\-region\fR
+chr3:2500\-3000' (two regions)'
+.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/createmanpages b/debian/createmanpages
new file mode 100755
index 0000000..b8ed6b4
--- /dev/null
+++ b/debian/createmanpages
@@ -0,0 +1,22 @@
+#!/bin/sh
+MANDIR=debian
+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 $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+progname=configManta
+help2man --no-info --no-discard-stderr --help-option=" --allHelp" \
+         --name='configure the Manta SV analysis pipeline' \
+            --version-string="$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..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1

-- 
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