[med-svn] [Git][med-team/atropos][master] 2 commits: Add manpage

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / atropos


Commits:
408e0789 by Andreas Tille at 2019-04-12T14:51:27Z
Add manpage

- - - - -
5c30dd0d by Andreas Tille at 2019-04-12T15:04:31Z
Upload to unstable

- - - - -


4 changed files:

- + debian/atropos.1
- debian/changelog
- + debian/createmanpages
- + debian/manpages


Changes:

=====================================
debian/atropos.1
=====================================
@@ -0,0 +1,50 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH ATROPOS "1" "April 2019" "atropos 1.1.21" "User Commands"
+.SH NAME
+atropos \- NGS read trimming tool that is specific, sensitive, and speedy
+.SH SYNOPSIS
+.B atropos
+[\-\-config <config file>] <command> [options]
+.SH OPTIONS
+.SS commands
+.TP
+detect:
+Detect adapter sequences directly from read sequences. Use this
+command if you are unsure if your data has adapters, or if you know that it
+has adapters but you don't know what are the adapter sequences.
+.TP
+error:
+Estimate the sequencing error rate. Use this command to help determine
+the quality of your data, and to decide the value for the max error rate (\fB\-e\fR)
+parameter. Normal error for an Illumina experiment is around 1% or less. We
+recommend setting \fB\-e\fR to 10x the empirical error rate.
+.TP
+qc:
+Compute read\-level statistics. The output is identical to running the
+\&'trim' command with '\-\-stats pre'. Use this command to get an idea of the
+quality of your raw data.
+.TP
+trim:
+Trim adapters and low\-quality bases, and perform other NGS
+preprocessing. This command provides most of Atropos' functionality.
+.SS optional arguments
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-\-config\fR <config file>
+provide options in a config file
+.P
+Use "atropos <command> \fB\-\-help\fR" to see all options for a specific command.
+See http://atropos.readthedocs.org/ for full documentation.
+.SH SEE ALSO
+Atropos is a fork of Cutadapt 1.10 (
+https://github.com/marcelm/cutadapt/tree/2f3cc0717aa9ff1e0326ea6bcb36b712950d4999)
+by John Didion, et al., "Atropos: sensitive, specific, and speedy trimming of
+NGS reads, submitted.
+.PP
+Cutadapt (https://github.com/marcelm/cutadapt) was developed by Marcel Martin,
+"Cutadapt Removes Adapter Sequences From High\-Throughput Sequencing Reads,"
+EMBnet Journal, 2011, 17(1):10\-12.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.


=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-atropos (1.1.21+dfsg-1) UNRELEASED; urgency=medium
+atropos (1.1.21+dfsg-1) unstable; urgency=medium
 
-  * Initial release (Closes: #<bug>)
+  * Initial release (Closes: #926944)
 
- -- Andreas Tille <tille at debian.org>  Fri, 12 Apr 2019 13:25:32 +0200
+ -- Andreas Tille <tille at debian.org>  Fri, 12 Apr 2019 17:04:21 +0200


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,27 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and
+can be used for any other usage of the program.
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" " \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT


=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1



View it on GitLab: https://salsa.debian.org/med-team/atropos/compare/062f39d62f362b8375b708fca0b8d020f27edb4d...5c30dd0d5138158e2243a8733a4047743c48e413

-- 
View it on GitLab: https://salsa.debian.org/med-team/atropos/compare/062f39d62f362b8375b708fca0b8d020f27edb4d...5c30dd0d5138158e2243a8733a4047743c48e413
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