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<tool id="quast" name="Quast" version="1.0.0" >
	<description>QUAST (Quality ASsessment Tool) evaluates genome assemblies.</description>
		
	<requirements>
		<requirement type="package" version="3.2">quast</requirement>
	</requirements>

	<stdio>
	    <exit_code range="1:" level="fatal" description="The tool's exit code was 1, which suggests that something went wrong." />
	</stdio>

	<command>		
		quast.py 
		 -o outputdir
		
		#if $gene_selection == "eukaryote" :
			--eukaryote
		#end if
		
		#if $gene_selection == "Metagenes" :
			--meta
                #end if
		
		--min-contig $min_contig
		
		
		#for $i in $files:
			$i.input
		#end for
		;
		cp outputdir/report.txt $quast_out;
	</command>
	
	<inputs>
		<repeat name="files" title="Input contig files">	
			<param type="data" format="fasta" name="input" label="Contigs output file"/>	
		</repeat>
		<param name="gene_selection" type="select">
			<option value="prokaryotes">Prokaryotes</option>
			<option value="eukaryote">Eukaryote</option>
			<option value="metagenes">Metagenomes</option>
		</param>
		<param name="min_contig" type="integer" value="500" label="Set the threshold for the contig length (default is 500)"/>
	</inputs>
	
	<outputs>
		<data format="txt" name="quast_out" label="Quast report.txt" from_work_dir="Quast_report.txt"/>
	</outputs>

	<tests>
		<test>
			<param name="input" value="input_contigs_1.fasta"/>
			<param name="gene_selection" value="eukaryote"/>
			<param name="min_config" value="500"/>
			<output name="quast_out" file="output_Quast_report.txt"/>
		</test>
	</tests>
	
	<help>
**Description**
		
Galaxy tool wrapper for the QUAST tool. Quast stands for QUality ASsessment Tool. It evalutes genome assemblies by computing various metrics. 
For more information regarding the settings of the tool, please visit the QUAST 3.2 Manual on http://quast.bioinf.spbau.ru/manual.html

-----

**Inputs and Outputs**
		
- Input:
	+ The tool accepts assemblies and references in FASTA format. 

- Output:
	+ An assessment summary in plain text format


-----

**Tool Information**

- QUAST Tool v3.2: 
	+ Release Date: November 2015
	+ URL: http://bioinf.spbau.ru/quast
	+ Source URL: https://downloads.sourceforge.net/project/quast/quast-3.2.tar.gz

-----
		
**QUAST Galaxy Wrapper Author and Contact Information**

+ Jacob Jablonski
+ AAFC-MBB Team
+ Email: [e-mail]
+ Agriculture and Agri-foods Canada, Ottawa, ON, Canada

	</help> 

	<citations>
		<citation type="bibtex">@ARTICLE{a1,
		author = {Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler},
		title = {QUAST: quality assessment tool for genomce assemblies, Bioinformatics (2013) 29 (8): 1072-1075}
		}</citation>
	</citations>  
</tool>