[med-svn] [Git][med-team/nanofilt][master] Add manpages

[Shayan Doust]

Shayan Doust pushed to branch master at Debian Med / nanofilt


Commits:
987790d4 by Shayan Doust at 2020-06-16T18:40:31+01:00
Add manpages

- - - - -


2 changed files:

- + debian/mans/NanoFilt.1
- + debian/nanofilt.manpages


Changes:

=====================================
debian/mans/NanoFilt.1
=====================================
@@ -0,0 +1,76 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
+.TH NANOFILT "1" "June 2020" "NanoFilt 2.6.0" "User Commands"
+.SH NAME
+NanoFilt \- filtering and trimming of long read sequencing data
+.SH DESCRIPTION
+usage: NanoFilt [\-h] [\-v] [\-\-logfile LOGFILE] [\-l LENGTH]
+.IP
+[\-\-maxlength MAXLENGTH] [\-q QUALITY] [\-\-minGC MINGC]
+[\-\-maxGC MAXGC] [\-\-headcrop HEADCROP] [\-\-tailcrop TAILCROP]
+[\-s SUMMARY] [\-\-readtype {1D,2D,1D2}]
+[input]
+.PP
+Perform quality and/or length and/or GC filtering of (long read) fastq data.           Reads on stdin.
+.SS "General options:"
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+show the help and exit
+.TP
+\fB\-v\fR, \fB\-\-version\fR
+Print version and exit.
+.TP
+\fB\-\-logfile\fR LOGFILE
+Specify the path and filename for the log file.
+.TP
+input
+input, uncompressed fastq file
+.SS "Options for filtering reads on.:"
+.TP
+\fB\-l\fR LENGTH, \fB\-\-length\fR LENGTH
+Filter on a minimum read length
+.TP
+\fB\-\-maxlength\fR MAXLENGTH
+Filter on a maximum read length
+.TP
+\fB\-q\fR QUALITY, \fB\-\-quality\fR QUALITY
+Filter on a minimum average read quality score
+.TP
+\fB\-\-minGC\fR MINGC
+Sequences must have GC content >= to this. Float between 0.0 and 1.0. Ignored if
+using summary file.
+.TP
+\fB\-\-maxGC\fR MAXGC
+Sequences must have GC content <= to this. Float between 0.0 and 1.0. Ignored if
+using summary file.
+.SS "Options for trimming reads.:"
+.TP
+\fB\-\-headcrop\fR HEADCROP
+Trim n nucleotides from start of read
+.TP
+\fB\-\-tailcrop\fR TAILCROP
+Trim n nucleotides from end of read
+.SS "Input options.:"
+.TP
+\fB\-s\fR SUMMARY, \fB\-\-summary\fR SUMMARY
+Use albacore or guppy summary file for quality scores
+.TP
+\fB\-\-readtype\fR {1D,2D,1D2}
+Which read type to extract information about from summary. Options are 1D, 2D or
+1D2
+.SS "EXAMPLES:"
+.IP
+gunzip \fB\-c\fR reads.fastq.gz | NanoFilt \fB\-q\fR 10 \fB\-l\fR 500 \fB\-\-headcrop\fR 50 | minimap2 genome.fa \- | samtools sort \fB\-O\fR BAM \- at 24 \fB\-o\fR alignment.bam \-
+gunzip \fB\-c\fR reads.fastq.gz | NanoFilt \fB\-q\fR 12 \fB\-\-headcrop\fR 75 | gzip > trimmed\-reads.fastq.gz
+gunzip \fB\-c\fR reads.fastq.gz | NanoFilt \fB\-q\fR 10 | gzip > highQuality\-reads.fastq.gz
+.SH "SEE ALSO"
+The full documentation for
+.B NanoFilt
+is maintained as a Texinfo manual.  If the
+.B info
+and
+.B NanoFilt
+programs are properly installed at your site, the command
+.IP
+.B info NanoFilt
+.PP
+should give you access to the complete manual.


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debian/nanofilt.manpages
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+debian/mans/*.1



View it on GitLab: https://salsa.debian.org/med-team/nanofilt/-/commit/987790d41c2a7b6ee0d871f1737827c086708498

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