<tool id="cg_testvariants" name="testvariants(beta) 1.6" version="1.0.1">
<!--
This tool creates a GUI for the testvariants function of cgatools from Complete Genomics, Inc.
written 6-18-2012 by bcrain@completegenomics.com
updated 8-14-2012 by bcrain@completegenomics.com
-->

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

  <command>
<!-- print version of cgatools to STDOUT-->
cgatools | head -1;

<!-- print command lines to STDOUT-->
echo "cgatools testvariants --beta
--reference ${crr.fields.path}
--output $output
--input $listing
--variants 
#if $data_sources.data_source == "in" <!--data in galaxy-->
#for $v in $data_sources.file_types.files <!--get each var/mastervar file-->
${v.input}
#end for
#else <!--data outside galaxy-->
`cat $data_sources.list`
#end if
";

<!-- execute cgatools-->
cgatools testvariants
--beta
--reference ${crr.fields.path}
--output $output
--input $listing
--variants 
#if $data_sources.data_source == "in" <!--data in galaxy-->
  #for $v in $data_sources.file_types.files <!--get each var/mastervar file-->
    ${v.input}
  #end for
#else <!--data outside galaxy-->
  `cat $data_sources.list`
#end if
  </command>

  <outputs>
    <data format="tabular" name="output" label="${tool.name} output"/>
  </outputs>
  
  <inputs>
  	<!--form field to select crr file-->
    <param name="crr" type="select" label="Reference genome (.crr file)">
      <options from_data_table="cg_crr_files" />
    </param>

	  <!--form fields to select variant list-->
	  <param name="listing" type="data" format="tabular" label="Select variant list (output of listvariants)">
			<validator type="dataset_ok_validator" />
			<validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
				metadata_name="dbkey" metadata_column="1"
				message="cgatools is not currently available for this build."/>
	  </param>

		<!--conditional to select data in/outside galaxy-->
		<conditional name="data_sources">
			<param name="data_source" type="select" label="Where are the input files?">
				<option value="in" selected="true">imported into Galaxy</option>
				<option value="out">located outside Galaxy (data on server or mounted drive)</option>
			</param>
			
			<when value="in">
				<!--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>
					
					<!--form field to select variant files-->
					<when value="var">			
						<repeat name="files" title="Var file" min="1">
							<param name="input" type="data" format="cg_var" label="Dataset">
								<validator type="dataset_ok_validator" />
								<validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
									metadata_name="dbkey" metadata_column="1"
									message="cgatools is not currently available for this build."/>
							</param>
						</repeat>
					</when>
					
					<!--form field to select masterVar files-->
					<when value="mastervar">			
						<repeat name="files" title="MasterVar file" min="1">
							<param name="input" type="data" format="cg_mastervar" label="Dataset">
								<validator type="dataset_ok_validator" />
								<validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
									metadata_name="dbkey" metadata_column="1"
									message="cgatools is not currently available for this build."/>
							</param>
						</repeat>
					</when>
				</conditional>
			</when>
			
			<!--form field to enter list file-->
			<when value="out">
				<param name="list" type="text" label="Enter file containing list of var or masterVar files (/path/file)" size="200" help="This file should contain a list of var or masterVar files, one per line in the format /path/varfile (e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/var-GS00000YYYY-ASM.tsv.bz2), the var or masterVar files can be compressed (gz, bz2).">
					<validator type="empty_field" message="You must supply a file containing a list of var or masterVar files"/>
				</param>
			</when>
		</conditional>
  </inputs>

  <help>
  
**What it does**

This tool uses the cgatools testvariants to test var or masterVar files for the presence of variants.

**cgatools 1.6.0 Documentation**

Userguide: http://cgatools.sourceforge.net/docs/1.6.0/cgatools-user-guide.pdf

Release notes: http://cgatools.sourceforge.net/docs/1.6.0/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>