<tool id="intertek_flapjack_snp_sample_processor" name="Intertek / Flapjack - SNP Sample File Processor" version="0.0.1">
	<description>convert an HDF5 formatted genotype file into a Flapjack formatted genotype file</description>
	<command><![CDATA[
		java
		#if $adv_opts.show_advanced
			-Xmx$adv_opts.memory
		#end if
		-cp $__tool_directory__/lib/flapjack.jar jhi.flapjack.io.cmd.IntertekFlapjackSnpSampleFileProcessor
		-g $genotype
		-i $intertek
		-o $output
	]]></command>
	<inputs>
		<param format="txt" name="intertek" type="data" label="Favourable allele file"
			help="An Intertek file with favourable and unfavourable allele information for markers."/>
		<param format="fjgenotype" name="genotype" type="data" label="Flapjack genotype file"
			help="A Flapjack formatted genotype file with markers which match those in the intertek file so that we can
				add the favourable and unfavourable allele information to this Flapjack genotype file."
			optional="true"/>

		<conditional name="adv_opts">
			<param name="show_advanced" type="boolean"
				   label="Enable advanced options"
				   truevalue="show" falsevalue="">
			</param>
			<when value="show">
				<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>
	</inputs>

	<outputs>
		<data format="fjgenotype" 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: http://flapjack.hutton.ac.uk/en/latest/projects_&_data_formats.html
	]]></help>

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