<tool id="cg_testvariants" name="TestVariants" version="1.7.1">

	<description>Test for the presence of variants</description> 

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

	<command> <!--run executable-->
		cgatools | head -1;
		cgatools testvariants
		--beta
		--reference ${crr.fields.crr_path}
		--output $output
		--input $listing
		--variants 
		#for $v in $file_types.varfiles <!--get each var/mastervar file-->
			${v.input}
		#end for
	</command>
  
	<inputs>
  	<!--form field to select crr file-->
		<param name="crr" type="select" label="Reference Build">
			<options from_data_table="cg_anno_files" />
		</param>

		<!--form fields to select variant list-->
		<param name="listing" type="data" format="tabular" label="Select variant list"/>			

		<!--conditional to select input file type-->
		<conditional name="file_types">
			<param name="file_type" type="select" label="Select the input file type">
				<option value="var" selected="true">var files</option>
				<option value="mastervar">mastervar files</option>
			</param>
			<when value="var">			
				<repeat name="varfiles" title="Variant files">
					<param name="input" type="data" format="cg_var" label="Dataset"/>
				</repeat>
			</when>
			<when value="mastervar">						
				<repeat name="varfiles" title="Variant files">
					<param name="input" type="data" format="cg_mastervar" label="Dataset"/>				
				</repeat>
			</when>
		</conditional>

		<!-- prefix for output file so you dont have to manually rename history items -->
		<param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>	
	</inputs>

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

	<help>
**What it does**

This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants.

**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
		  testvariants - Tests variant files for presence of variants.
		
		DESCRIPTION
		  Tests variant files for presence of variants. The output is a tab-delimited
		  file consisting of the columns of the input variants file, plus a column 
		  for each assembly results file that contains a character code for each 
		  allele. The character codes have meaning as follows:
			
		    0 This allele of this genome is consistent with the reference at this 
		      locus but inconsistent with the variant.
		    1 This allele of this genome has the input variant at this locus.
		    N This allele of this genome has no-calls but is consistent with the 
		      input variant.
		
		OPTIONS
		  -h [ --help ] 
		      Print this help message.
		
		  --beta 
		      This is a beta command. To run this command, you must pass the --beta 
		      flag.
		
		  --reference arg
		      The reference crr file.
		
		  --input arg (=STDIN)
		      The input variants to test for.
		
		  --output arg (=STDOUT)
		      The output file (may be omitted for stdout).
		
		  --variants arg
		      The input variant files (may be passed in as arguments at the end of 
		      the command).
		
		SUPPORTED FORMAT_VERSION
		  0.3 or later
	</help>
</tool>