<tool id="flapjack_mabcstats" name="Flapjack MABCStats" version="0.0.1">

  <description>Run marker assisted backcrossing analysis on a dataset</description>

  <command><![CDATA[
  java
  #if $advanced_options.show_advanced
    -Xmx$advanced_options.memory
  #end if
  -cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.GenerateMabcStats
  -m $map
  -g $genotypes
  -q $qtls
  -r $parent1
  -d $parent2
  -model $model
  -c $coverage
  #if $advanced_options.show_advanced
    $advanced_options.decimalEnglish
  #end if
  -o $output
  #if $create_project  
    -p $project
  #end if	
  ]]></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 format="fjqtl" name="qtls" type="data" label="Flapjack QTL file"
		help="Flapjack-formatted (tab-delimited text) input file of QTL data"/>
	<param name="parent1" type="integer" value="1" label="Index of recurrent parent"
		help="The index of the recurrent parent in the genotype file"/>
	<param name="parent2" type="integer" value="2" label="Index of donor parent"
		help="The index of the donor parent in the genotype file"/>
	<param name="model" type="select" label="Model"
		help="The model to use for calculating statistics">
	  <option selected="true" value="weighted">Weighted</option>
	  <option value="unweighted">Unweighted</option>
	</param>
	<param name="coverage" type="float" value="10" label="Maximum coverage of a marker"
		help="The maximum length of genome a marker can represent"/>
	<conditional name="advanced_options">
		<param name="show_advanced" type="boolean" label="Enable advanced options"
			truevalue="show" falsevalue="">
		</param>
		<when value="show">
			<param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="True"
            label="Force English-style decimal marks"
            help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy's locale settings"/>
			<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>
		</when>
	</conditional>
	
	<param name="create_project" type="boolean" label="Also create Flapjack project file"
		truevalue="true" falsevalue="false" help="Creates an additional Flapjack project file containing the MABC results.">
	</param>
  </inputs>
  
  <outputs>
    <data format="tabular" name="output" />
	<data format="flapjack" name="project">
		<filter>create_project</filter>
	</data> 
	
  </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>