<tool id="cg_decodecrr" name="DecodeCRR" version="1.7.1">

	<description>retreives the sequence for a given range of a chromosome.</description> 

	<requirements>		
		<requirement type="package" version="1">cgatools17</requirement>
	</requirements>

	<command>
		cgatools | head -1;
		cgatools decodecrr 
		#if $refcrr.reference == "custom":
		--reference $refcrr.customcrr
		#else:
		--reference ${refcrr.reffile.fields.crr_path} 		 
		#end if			
		--output $output 
		--range $range	
	</command>

	<inputs>
		<conditional name="refcrr">
			<param name="reference" type="select" label="Reference">
				<option value="builtin" > Built-in Reference CRR </option>
				<option value="custom"> Custom CRR file </option>						
			</param>
			<when value="builtin">
				<param name="reffile" type="select" label="Reference">
					<options from_data_table="cg_anno_files" />								
				</param>
			</when>
			<when value="custom">
				<param name="customcrr" type="data" format="crr" label="Select custom crr file" />
			</when>
		</conditional>

		<param name="range" type="text" label="Select range" size="15" help="chr:begin-end e.g. chr4:30722030-30726957" />
		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>			
	</inputs>

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

	<help> 
	
**What it does**

Retrieves the sequence for a given range of a chromosome.

**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
    decodecrr - Prints the reference sequence for a given reference range.

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

  --reference arg
        The reference crr file (may be passed in as argument at the end of the 
        command).

  --output arg (=STDOUT)
        The output file (may be omitted for stdout).

  --range arg
        The range of bases to print (chr,begin,end or chr:begin-end).

	</help>
</tool>