changeset 31:503e4165b1fc

Uploaded

--- a/featurecounts_valid_gff.xml	Fri Feb 07 04:34:48 2014 -0500
+++ b/featurecounts_valid_gff.xml	Fri Feb 07 05:00:14 2014 -0500
@@ -118,21 +118,51 @@
 	</outputs>
 	
 	<help>
-featureCounts-valid-gff:
-	This application count reads aligned to annotated genes in a reference genome from SAM or BAM files.
-	This is similar to tools like DEXSeq-count, HTSeq-count, etc.
-	The tool is written in pure C, without the requirement of third party sorting software.
-	Therefore this tool is incredibly fast and takes about 7 minutes on a single average CPU for a 10GB alignment to a Homo Sapiens genome!
-	
-	---
-	
-	Remark that this is a fork of the original "featureCounts" package, which can be found at:
-	http://subread.sourceforge.net/
-	
-	---
-	
-	This fork is able to read GTF/GFF files according to the provided standard by Ensembl, which can be found at:
-	http://www.ensembl.org/info/website/upload/gff.html
-	The fork is maintained by: Youri Hoogstrate
-	</help>
+featureCounts-valid-gff::
+
+**featureCounts Overview**
+FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files.
+It has a variety of advanced parameters but its major strength is its outstanding performance: analysis of a 10GB BAM file takes about 7 minutes on a single average CPU (Homo Sapiens genome)!
+Liao Y, Smyth GK and Shi W. featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics, Advance Access, accepted on Nov 7, 2013
+
+featureCounts is part of a bigger analysis suite called subread:
+http://subread.sourceforge.net/
+Liao Y, Smyth GK and Shi W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Research, 41(10):e108, 2013
+
+The tool requires a GFF/GTF file for getting the genomic coordinates of the genes that should be measured.
+This file format is known to have at least the following common variants:
+* http://genome.ucsc.edu/FAQ/FAQformat.html#format3
+* http://www.ensembl.org/info/website/upload/gff.html
+
+FeatureCounts is only able to handle the UCSC variant. Therefore the project was forked to "featureCounts-valid-gff", able to handle both.
+Whis wrapper wraps the fork, such that it is independent of the GFF/GTF variant.
+
+**Input formats**
+
+Alignments should be provided in either:
+* SAM format - hhttp://samtools.sourceforge.net/samtools.shtml#5
+* BAM format
+
+Gene regions should be provided in the GFF/GTF format:
+* http://genome.ucsc.edu/FAQ/FAQformat.html#format3
+* http://www.ensembl.org/info/website/upload/gff.html
+
+**Installation**
+
+Make sure you have proper GFF/GTF files (corresponding to your reference genome used for the aligment) uploaded to your history.
+The source of this file should not be important since this fork can handle both ENSEMBL and UCSC variants of the GTF/GFF format.
+
+**License**
+
+* featureCounts / subread: GNU General Public License version 3.0 (GPLv3)
+* featureCounts-valid-gff: GNU General Public License version 3.0 (GPLv3)
+
+**Contact**
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project:
+http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
+
+More tools by the Translational Research IT (TraIT) project can be found in the following repository:
+http://toolshed.nbic.nl/
+</help>
 </tool>