<tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1">

<!--System.out.println("Usage: pedverf1sstats <options>\n"
				+ " where valid options are:\n"
				+ "   -map=<map_file>                (required input file)\n"
				+ "   -genotypes=<genotypes_file>    (required input file)\n"
				+ "   -parent1=<index_of_line>       (required parameter, first line is index 1)\n"
				+ "   -parent2=<index_of_line>       (required parameter, first line is index 1)\n"
				+ "   -expectedf1=<index_of_line>    (optional parameter, first line is index 1)\n"
				+ "   -decimalEnglish                (optional parameter)\n"
				+ "   -output=<output_file>          (required output file)\n");-->

  <description>Run pedigree verification of F1s (known parents) analysis</description>
  <command><![CDATA[
  java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GeneratePedVerF1sStats 
  -map=$map -genotypes=$genotypes -parent1=$parent1 -parent2=$parent2 
  #if $simulate_f1.simulate_f1_selector == "file":
	-expectedf1=$simulate_f1.expectedF1
  #end if
  $decimalEnglish -output=$output
  ]]>
  </command>
  <inputs>
    <param format="fjmap" name="map" type="data" label="Flapjack map file"
		help="Flapjack-formatted (tab-delimited text) input file of map data"/>
	<param format="fjgenotype" name="genotypes" type="data" label="Flapjack genotype file"
		help="Flapjack-formatted (tab-delimited text) input file of genotype data"/>
	<param name="parent1" type="integer" value="1" label="Index of parent 1"
		help="The index of the first parent in the genotype file"/>
	<param name="parent2" type="integer" value="2" label="Index of parent 2"
		help="The index of the second parent in the genotype file"/>
		
	<conditional name="simulate_f1">
		<param name="simulate_f1_selector" type="select" label="Simulate expected F1 (or use F1 from file)">
			<option value="simulate" selected="True">Simulate</option>
			<option value="file">Select from file</option>
		</param>
		<when value="file">
			<param argument="-expectedF1" type="integer" value="3" label="Index of expected F1"
			help="The index of the donor parent in the genotype file"/>
		</when>
	</conditional>

	<param argument="decimalEnglish" type="boolean" truevalue="-decimalEnglish" falsevalue="" checked="True"
            label="Read input data using decimal English"
            help="Build the index using a perfect hash rather than a dense hash.  This will require less memory
			(especially during quantification), but will take longer to construct "/>
	<param name="memory" type="select" label="Memory"
		help="How much memory to use; larger files may require more memory">
	  <option selected="true" value="64m">64MB</option>
	  <option value="128m">128MB</option>
	  <option value="256m">256MB</option>
	</param>
  </inputs>
  <outputs>
    <data format="tabular" name="output" />
  </outputs>
  
  <stdio>
    <exit_code range="1:" />
  </stdio>

  <help><![CDATA[
.. class:: infomark

**What it does**

Flapjack is a multi-platform application providing interactive visualizations of high-throughput genotype data,
allowing for rapid navigation and comparisons between lines, markers and chromosomes.

This tool converts a Flapjack-formatted file of genotype data into a corresponding HDF5 file.
See Flapjack's documentation_ for more details on the various Flapjack data formats.

.. _documentation: https://ics.hutton.ac.uk/wiki/index.php/Flapjack_Help_%2D_Projects_and_Data_Formats 



  ]]></help>
  <citations>
    <citation type="doi">10.1093/bioinformatics/btq580</citation>
  </citations>
</tool>