<tool id="flapjack_createproject" name="Flapjack CreateProject" version="0.0.1">

<!--System.out.println("Usage: createproject <options>\n"
				+ " where valid options are:\n"
				+ "   -map=<map_file>                (optional input file)\n"
				+ "   -genotypes=<genotypes_file>    (required input file)\n"
				+ "   -traits=<traits_file>          (optional input file)\n"
				+ "   -qtls=<qtl_file>               (optional input file)\n"
				+ "   -decimalEnglish                (optional input parameter)\n"
				+ "   -project=<project_file>        (required output file)\n");-->

  <description>Run pedigree verification of F1s (known parents) analysis</description>
  <command><![CDATA[
  java -Xmx$memory -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.CreateProject 
  -map=$map -genotypes=$genotypes
##  -galaxyHTML=$html 
  -project=$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 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>
  <!-- label="${tool.name} on ${on_string}: project.flapjack" -->
    <data name="output" format="flapjack" />
	<!--<data name="html" format="html" />-->
  </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 creates a Flapjack project file from the supplied tab-delimitted flapjack input files.
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>