[med-svn] [Git][med-team/qcat][master] 2 commits: Add manpages
Andreas Tille
gitlab at salsa.debian.org
Wed Apr 22 09:51:41 BST 2020
Andreas Tille pushed to branch master at Debian Med / qcat
Commits:
73529cc6 by Andreas Tille at 2020-04-22T10:16:21+02:00
Add manpages
- - - - -
1b8e86c5 by Andreas Tille at 2020-04-22T10:51:21+02:00
Add some missing (Build-)Depends
- - - - -
8 changed files:
- debian/control
- debian/copyright
- + debian/createmanpages
- + debian/man/qcat-eval-truth.1
- + debian/man/qcat-eval.1
- + debian/man/qcat-roc.1
- + debian/man/qcat.1
- + debian/manpages
Changes:
=====================================
debian/control
=====================================
@@ -9,7 +9,10 @@ Build-Depends: debhelper-compat (= 12),
python3-setuptools,
python3-pytest-runner <!nocheck>,
python3-pytest <!nocheck>,
- python3-pytest-cov <!nocheck>
+ python3-pytest-cov <!nocheck>,
+ python3-biopython <!nocheck>,
+ python3-parasail <!nocheck>,
+ python3-yaml <!nocheck>
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/qcat
Vcs-Git: https://salsa.debian.org/med-team/qcat.git
@@ -19,7 +22,9 @@ Package: qcat
Architecture: all
Depends: ${python3:Depends},
${misc:Depends},
- python3-parasail
+ python3-biopython,
+ python3-parasail,
+ python3-yaml
Description: demultiplexing Oxford Nanopore reads from FASTQ files
Qcat is a command-line tool for demultiplexing Oxford Nanopore reads
from FASTQ files. It accepts basecalled FASTQ files and splits the reads
=====================================
debian/copyright
=====================================
@@ -3,7 +3,7 @@ Upstream-Name: qcat
Source: https://github.com/nanoporetech/qcat/releases
Files: *
-Copyright: 20xx-20yy <upstream>
+Copyright: 2018-2020 by Oxford Nanopore Technologies Ltd.
License: MPL-2.0
Files: debian/*
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,46 @@
+#!/bin/sh
+MANDIR=debian/man
+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\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=qcat-eval
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Command line interface to barcode detection library" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=qcat-eval-truth
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Command line interface to barcode detection library" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+progname=qcat-roc
+help2man --no-info --no-discard-stderr --help-option=" -h" \
+ --name="Command line interface to barcode detection library" \
+ --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/man/qcat-eval-truth.1
=====================================
@@ -0,0 +1,27 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH QCAT-EVAL-TRUTH "1" "April 2020" "qcat-eval-truth 1.1.0" "User Commands"
+.SH NAME
+qcat-eval-truth \- Command line interface to barcode detection library
+.SH DESCRIPTION
+WARNING:root:Could not load pysam. To use qcat\-eval\-full please install mappy.
+usage: qcat\-eval\-truth [\-h] \fB\-t\fR TSV \fB\-n\fR NAME \fB\-g\fR GENOMES [\-\-max MAX] [FASTQ]
+.PP
+Command line interface to barcode detection library
+.SS "positional arguments:"
+.IP
+FASTQ
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.HP
+\fB\-t\fR TSV, \fB\-\-tsv\fR TSV
+.HP
+\fB\-n\fR NAME, \fB\-\-name\fR NAME
+.HP
+\fB\-g\fR GENOMES, \fB\-\-genomes\fR GENOMES
+.HP
+\fB\-\-max\fR MAX
+.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/man/qcat-eval.1
=====================================
@@ -0,0 +1,33 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH QCAT-EVAL "1" "April 2020" "qcat-eval 1.1.0" "User Commands"
+.SH NAME
+qcat-eval \- Command line interface to barcode detection library
+.SH DESCRIPTION
+usage: qcat\-eval [\-h] [\-t TSV] [\-n NAME] [\-d DATASET] [\-s] [\-g GUPPY]
+.IP
+[\-i INCORRECT]
+[FASTQ]
+.PP
+Command line interface to barcode detection library
+.SS "positional arguments:"
+.IP
+FASTQ
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.HP
+\fB\-t\fR TSV, \fB\-\-tsv\fR TSV
+.HP
+\fB\-n\fR NAME, \fB\-\-name\fR NAME
+.HP
+\fB\-d\fR DATASET, \fB\-\-dataset\fR DATASET
+.HP
+\fB\-s\fR, \fB\-\-summary\fR
+.HP
+\fB\-g\fR GUPPY, \fB\-\-guppy_summary\fR GUPPY
+.HP
+\fB\-i\fR INCORRECT, \fB\-\-get\-incorrect\fR INCORRECT
+.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/man/qcat-roc.1
=====================================
@@ -0,0 +1,18 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH QCAT-ROC "1" "April 2020" "qcat-roc 1.1.0" "User Commands"
+.SH NAME
+qcat-roc \- Command line interface to barcode detection library
+.SH DESCRIPTION
+usage: qcat\-roc [\-h] [FASTQ]
+.PP
+Command line interface to barcode detection library
+.SS "positional arguments:"
+.IP
+FASTQ
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.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/man/qcat.1
=====================================
@@ -0,0 +1,101 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.
+.TH QCAT "1" "April 2020" "qcat 1.1.0" "User Commands"
+.SH NAME
+qcat \- demultiplexing Oxford Nanopore reads from FASTQ files
+.SH DESCRIPTION
+usage: qcat [\-h] [\-V] [\-l LOG] [\-\-quiet] [\-f FASTQ] [\-b BARCODE_DIR]
+.IP
+[\-o OUTPUT] [\-\-min\-score MIN_QUAL] [\-\-detect\-middle] [\-t THREADS]
+[\-\-min\-read\-length MIN_LENGTH] [\-\-tsv] [\-\-trim]
+[\-k {Auto,RAB204/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001}]
+[\-\-list\-kits] [\-\-guppy | \fB\-\-epi2me\fR | \fB\-\-dual\fR | \fB\-\-simple]\fR
+[\-\-no\-batch] [\-\-filter\-barcodes]
+[\-\-simple\-barcodes SIMPLE_BARCODES]
+.PP
+Python command\-line tool for demultiplexing Oxford Nanopore reads from FASTQ files
+.SS "optional arguments:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show this help message and exit
+.TP
+\fB\-V\fR, \fB\-\-version\fR
+show program's version number and exit
+.TP
+\fB\-l\fR LOG, \fB\-\-log\fR LOG
+Print debug information
+.TP
+\fB\-\-quiet\fR
+Don't print summary
+.SS "General settings:"
+.TP
+\fB\-f\fR FASTQ, \fB\-\-fastq\fR FASTQ
+Barcoded read file
+.TP
+\fB\-b\fR BARCODE_DIR, \fB\-\-barcode_dir\fR BARCODE_DIR
+If specified, qcat will demultiplex reads to this
+folder
+.TP
+\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
+Output file trimmed reads will be written to (default:
+stdout).
+.TP
+\fB\-\-min\-score\fR MIN_QUAL
+Minimum barcode score. Barcode calls with a lower
+score will be discarded. Must be between 0 and 100.
+(default: 60)
+.TP
+\fB\-\-detect\-middle\fR
+Search for adapters in the whole read
+.TP
+\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
+Number of threads. Only works with in guppy mode
+.TP
+\fB\-\-min\-read\-length\fR MIN_LENGTH
+Reads short than <min\-read\-length> after trimming will
+be discarded.
+.TP
+\fB\-\-tsv\fR
+Prints a tsv file containing barcode information each
+read to stdout.
+.TP
+\fB\-\-trim\fR
+Remove adapter and barcode sequences from reads.
+.TP
+\fB\-k\fR {Auto,RAB204/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001}, \fB\-\-kit\fR {Auto,RAB204/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001}
+Sequencing kit. Specifying the correct kit will
+improve sensitivity and specificity and runtime
+(default: auto)
+.TP
+\fB\-\-list\-kits\fR
+List all supported kits
+.SS "Demultiplexing modes:"
+.TP
+\fB\-\-guppy\fR
+Use Guppy's demultiplexing algorithm (default: false)
+.TP
+\fB\-\-epi2me\fR
+Use EPI2ME's demultiplexing algorithm (default: true)
+.TP
+\fB\-\-dual\fR
+Use dual barcoding algorithm
+.TP
+\fB\-\-simple\fR
+Use simple demultiplexing algorithm. Only looks for
+barcodes, not for adapter sequences. Use only for
+testing purposes!
+.SS "EPI2ME options (only valid with --epi2me):"
+.TP
+\fB\-\-no\-batch\fR
+Don't use information from multiple reads for kit
+detection (default: false)
+.TP
+\fB\-\-filter\-barcodes\fR
+Filter rare barcode calls when run in batch mode
+.SS "Simple options (only valid with --simple):"
+.TP
+\fB\-\-simple\-barcodes\fR SIMPLE_BARCODES
+Use 12 (standard) or 96 (extended) barcodes for
+demultiplexing
+.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/manpages
=====================================
@@ -0,0 +1 @@
+debian/man/*.1
View it on GitLab: https://salsa.debian.org/med-team/qcat/-/compare/a8162170a313cd4b504fc8fa1e1144c67fd620d0...1b8e86c5aa8e74d0b4096a06eca293edf9bc8c7a
--
View it on GitLab: https://salsa.debian.org/med-team/qcat/-/compare/a8162170a313cd4b504fc8fa1e1144c67fd620d0...1b8e86c5aa8e74d0b4096a06eca293edf9bc8c7a
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