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<?xml version="1.0" encoding="UTF-8"?>
<tool id="flaimapper" name="FlaiMapper" version="1.1.5.a">
	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
	<requirements>
		<requirement type="package" version="0.8.2.1">pysam</requirement>
		<requirement type="package" version="1.1.5">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>
	
	<stdio>
		<regex match="[fai_load] build FASTA index." source="stderr" level="log" />
	</stdio>
	
	<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,gff3" 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>
	
	<tests>
		<test>
			<param name="alignments" value="snord81.bam" />
			<param name="mask" value="ncrnadb09.gtf" format="gtf" />
			<param name="fasta" value="ncrnadb09.fa" format="fasta" />
			<param name="output_format" value="1" />
			
			<output name="output" file="snord81.flaimapper.txt" />
		</test>
	</tests>
	
	<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 FASTA format.

You can access **ncRNAdb09** at the following URLs:
https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*

Therefore you need bam files aligned to the same reference. We have made
the following available:

 - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
 - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz

If you want to test flaimapper with example data you can obtain several
alignment files from this following directory tree:

https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments

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

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).

	</help>
	
	<citations>
		<citation type="doi">10.1093/bioinformatics/btu696</citation>
	</citations>
</tool>