[med-svn] r12516 - trunk/packages/babraham/fastqc/trunk/debian

[Andreas Tille]

Author: tille
Date: 2012-11-08 10:28:43 +0000 (Thu, 08 Nov 2012)
New Revision: 12516

Added:
   trunk/packages/babraham/fastqc/trunk/debian/fastqc.1
   trunk/packages/babraham/fastqc/trunk/debian/manpages
Log:
Used help2man 2 create manpage (once the script was actually running)


Added: trunk/packages/babraham/fastqc/trunk/debian/fastqc.1
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/fastqc.1	                        (rev 0)
+++ trunk/packages/babraham/fastqc/trunk/debian/fastqc.1	2012-11-08 10:28:43 UTC (rev 12516)
@@ -0,0 +1,109 @@
+.TH FASTQC "1" "November 2012" "FastQC v0.10.1" "User Commands"
+.SH NAME
+FastQC \- high throughput sequence QC analysis tool
+.PP
+SYNOPSIS
+.IP
+fastqc seqfile1 seqfile2 .. seqfileN
+.IP
+fastqc [\-o output dir] [\-\-(no)extract] [\-f fastq|bam|sam]
+.IP
+[\-c contaminant file] seqfile1 .. seqfileN
+.PP
+.SH DESCRIPTION
+.IP
+FastQC reads a set of sequence files and produces from each one a quality
+control report consisting of a number of different modules, each one of
+which will help to identify a different potential type of problem in your
+data.
+.IP
+If no files to process are specified on the command line then the program
+will start as an interactive graphical application.  If files are provided
+on the command line then the program will run with no user interaction
+required.  In this mode it is suitable for inclusion into a standardised
+analysis pipeline.
+.IP
+The options for the program as as follows:
+.TP
+\fB\-h\fR \fB\-\-help\fR
+Print this help file and exit
+.TP
+\fB\-v\fR \fB\-\-version\fR
+Print the version of the program and exit
+.TP
+\fB\-o\fR \fB\-\-outdir\fR
+Create all output files in the specified output directory.
+Please note that this directory must exist as the program
+will not create it.  If this option is not set then the
+output file for each sequence file is created in the same
+directory as the sequence file which was processed.
+.TP
+\fB\-\-casava\fR
+Files come from raw casava output. Files in the same sample
+group (differing only by the group number) will be analysed
+as a set rather than individually. Sequences with the filter
+flag set in the header will be excluded from the analysis.
+Files must have the same names given to them by casava
+(including being gzipped and ending with .gz) otherwise they
+won't be grouped together correctly.
+.TP
+\fB\-\-extract\fR
+If set then the zipped output file will be uncompressed in
+the same directory after it has been created.  By default
+this option will be set if fastqc is run in non\-interactive
+mode.
+.TP
+\fB\-j\fR \fB\-\-java\fR
+Provides the full path to the java binary you want to use to
+launch fastqc. If not supplied then java is assumed to be in
+your path.
+.TP
+\fB\-\-noextract\fR
+Do not uncompress the output file after creating it.  You
+should set this option if you do not wish to uncompress
+the output when running in non\-interactive mode.
+.TP
+\fB\-\-nogroup\fR
+Disable grouping of bases for reads >50bp. All reports will
+show data for every base in the read.  WARNING: Using this
+option will cause fastqc to crash and burn if you use it on
+really long reads, and your plots may end up a ridiculous size.
+You have been warned!
+.TP
+\fB\-f\fR \fB\-\-format\fR
+Bypasses the normal sequence file format detection and
+forces the program to use the specified format.  Valid
+formats are bam,sam,bam_mapped,sam_mapped and fastq
+.TP
+\fB\-t\fR \fB\-\-threads\fR
+Specifies the number of files which can be processed
+simultaneously.  Each thread will be allocated 250MB of
+memory so you shouldn't run more threads than your
+available memory will cope with, and not more than
+6 threads on a 32 bit machine
+.TP
+\fB\-c\fR
+Specifies a non\-default file which contains the list of
+.TP
+\fB\-\-contaminants\fR
+contaminants to screen overrepresented sequences against.
+The file must contain sets of named contaminants in the
+form name[tab]sequence.  Lines prefixed with a hash will
+be ignored.
+.TP
+\fB\-k\fR \fB\-\-kmers\fR
+Specifies the length of Kmer to look for in the Kmer content
+module. Specified Kmer length must be between 2 and 10. Default
+length is 5 if not specified.
+.TP
+\fB\-q\fR \fB\-\-quiet\fR
+Supress all progress messages on stdout and only report errors.
+.PP
+.SH BUGS
+.IP
+Any bugs in fastqc should be reported either to simon.andrews at babraham.ac.uk
+or in www.bioinformatics.babraham.ac.uk/bugzilla/
+.SH AUTHOR
+.IP
+This manpage was created using \fBhelp2man\fR by Andreas Tille <tille at debian.org>
+for the Debian distribution but can be used by others as well.

Added: trunk/packages/babraham/fastqc/trunk/debian/manpages
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/babraham/fastqc/trunk/debian/manpages	2012-11-08 10:28:43 UTC (rev 12516)
@@ -0,0 +1 @@
+debian/*.1