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<?xml version="1.0" encoding="UTF-8"?>
<tool id="flaimapper" name="FlaiMapper" version="1.1.2.c">
	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
	<requirements>
		<requirement type="package" version="0.8.2.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! -->
		<requirement type="package" version="1.1.2">flaimapper</requirement>
	</requirements>
	
	<version_command>flaimapper --version</version_command>
	
	<command>
		flaimapper
			 -v
			 -f $output_format
			 -o $output
			 -m $mask
			 -r $fasta
		
		#for $alignment in $alignments
			$alignment
		#end for
	</command>
	
	<inputs>
		<param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
		
		<param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
			
		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
		
		<param name="output_format" type="select" label="Output format">
		<option value="1">Tabular (1 fragment per column)</option>
		<option value="2">Tabular (1 precursor per column)</option>
		<option value="3">GenBank</option>
		<!-- option value="gtf">GTF/GFF</option -->
		</param>
	</inputs>
	
	<outputs>
		<data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
	</outputs>
	
	<help>
FlaiMapper wrapper for Galaxy
=============================

https://github.com/yhoogstrate/flaimapper
http://www.ncbi.nlm.nih.gov/pubmed/25338717
http://dx.doi.org/10.1093/bioinformatics/btu696

Fragment Location Annotation Identification Mapper

FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.

Input formats
-------------
Alignments should be provided in BAM format.
Gene (MASK) 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

The reference sequence should be provided in FASTSA format.

Installation
------------

The wrapper makes use of easy_install to install a python egg. Please
ensure you have easy_install installed.

License
-------

**flaimapper** and **wrapper**:

GPL (>=3)

**pysam**:

The MIT License (>=3)

Contact
-------

The tool wrapper has been written by Youri Hoogstrate from the Erasmus
Medical Center (Rotterdam, Netherlands).


Development
-----------

* Repository-Maintainer: Youri Hoogstrate
* Repository-Developers: Youri Hoogstrate

* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools

The tool wrapper has been written by Youri Hoogstrate from the Erasmus
Medical Center (Rotterdam, Netherlands).

References
----------
**FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.**

*Hoogstrat* - Bioinformatics. 2014 Apr 1;30(7):923-30.

*Youri Hoogstrate, Guido Jenster, and Elena S. Martens-Uzunova* - Bioinformatics (2015) 31 (5): 665-673

- http://www.ncbi.nlm.nih.gov/pubmed/25338717
- http://dx.doi.org/10.1093/bioinformatics/btu696
	</help>
	
	<citations>
		<citation type="doi">10.1093/bioinformatics/btu696</citation>
	</citations>
</tool>