comparison featurecounts.xml @ 5:31279ea9fbfa draft

Uploaded

4:84fd5f7ec18f

		<data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
		<data format="text" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" />
	</outputs>
	
	<help>
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

**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**

1) Make sure you have proper GFF/GTF files (corresponding to your reference genome used for the aligment) uploaded to your history.

2) Make sure that your gene_sets.loc is configured properly as data table. This is generally done by copying the right information into: tool_data_table_conf.xml.
https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables

**Examples**

**References**

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.

Liao Y1, Smyth GK, Shi W.::

* http://www.ncbi.nlm.nih.gov/pubmed/24227677
* http://dx.doi.org/10.1093/bioinformatics/btt656


**License**

* featureCounts / subread: 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

I want to thank the Marius van den Beek for his contribution as well.

More tools by the Translational Research IT (TraIT) project can be found in the following repository:
http://toolshed.dtls.nl/

</help>
</tool>

5:31279ea9fbfa

		<data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
		<data format="text" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" />
	</outputs>
	
	<help>
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 SE BAM file takes about 7 minutes on a single average CPU (Homo Sapiens genome) [1].

Input formats
-------------
Alignments should be provided in either:

- SAM format, http://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
------------

1. Make sure you have proper GFF/GTF files (corresponding to your reference genome used for the aligment) uploaded to your history.

2. Make sure that your gene_sets.loc is configured properly as data table. This is generally done by copying the right information into: tool_data_table_conf.xml. More info at:  https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables

References
----------

**featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.**

*Liao Y1, Smyth GK, Shi W.* Bioinformatics. 2014 Apr 1;30(7):923-30.

- http://www.ncbi.nlm.nih.gov/pubmed/24227677
- http://dx.doi.org/10.1093/bioinformatics/btt656


License
-------

featureCounts / subread package:

- 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

I want to thank the Marius van den Beek for his contribution to this wrapper.

More tools by the Translational Research IT (TraIT) project can be found in the following repository:
http://testtoolshed.g2.bx.psu.edu/

</help>
</tool>