<tool id="fasta2crr" name="fasta-2-crr" version="1.7.1">
	<description> Convert fasta sequences into a single reference crr file </description>
	
	<requirements>
		<requirement type="package" version="1">cgatools17</requirement>
	</requirements>
	
	<command>
		cgatools | head -1;
		cgatools fasta2crr  
		#for $f in $fastafiles
			--input ${f.file}
		#end for 		
		--output $output 
		#if $circ != "None"
		--circular $circ 
		#end if	
	</command>
	
	<inputs>
		<repeat name="fastafiles" title="FASTA File" min="1">
			<param name="file" type="data" format="tsv" label="select input fasta file" />
		</repeat>
		<param name="circ" type="data" format="tsv,bz2" optional="true" label="select file containing comma-separated list of circular chromosome names"/>		
		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>					
	</inputs>

	<outputs>
		<data format="crr" name="output" label="$fname ${tool.name} on ${on_string}"/>
	</outputs>
	
	<help> 	

**What it does**

This tool converts input FASTA sequences into a single reference CRR file.

**cgatools 1.7.1 Documentation**

Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf

Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf

**Command line reference**::
	
		COMMAND NAME
		  fasta2crr - Converts fasta reference files to the crr format.

		OPTIONS
		  -h [ --help ] 
				Print this help message.

		  --input arg
				The input fasta files (may be passed in as arguments at the end of the 
				command, or omitted for stdin). Take care to specify the fasta files in
				chromosome order; ordering is important. To work with human Complete 
				Genomics data, the chromosome order should be chr1...chr22, chrX, chrY,
				chrM.

		  --output arg
				The output crr file.

		  --circular arg
				A comma-separated list of circular chromosome names. If ommitted, 
				defaults to chrM.

	</help>
</tool>