<tool id="flapjack_pedverstats" name="Flapjack PedVerStats" version="0.0.1">
	<description>run pedigree verification of F1s (known parents) analysis on a dataset</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.GeneratePedVerF1sStats
		-m $map
		-g $genotypes
		#if $qtls
			-q $qtls
		#end if
		#if $traits
			-t $traits
		#end if
		-f $parent1
		-s $parent2
		-o $output
		#if $simulate_f1.simulate_f1_selector == False
			-e $simulate_f1.expectedF1
		#end if
		#if $exclude_parents
			-x
		#end if
		#if $adv_opts.show_advanced
			$adv_opts.allChromosomes
			$adv_opts.collapseHets
			-M "$adv_opts.missingData"
			-S "$adv_opts.hetSep"
			$adv_opts.transposed
			$adv_opts.decimalEnglish
		#end if
		#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."
			   optional="true"/>

		<param format="fjphenotype" name="traits" type="data"
			   label="Flapjack Trait file"
			   help="Flapjack-formatted (tab-delimited text) input file of trait data."
			   optional="true"/>

		<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="boolean" label="Simulate expected F1 (or use F1 from file)"
				truevalue="" falsevalue="show" checked="true">
			</param>
			<when value="show">
				<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 name="exclude_parents" type="boolean" label="Exclude parental lines which have not been selected."
			   truevalue="true" falsevalue="false" help="Excludes parental lines which have not been selected as the recurrent, or donor parent from the analysis and results.">
		</param>

		<!-- WARNING: Below is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
		<conditional name="adv_opts">
			<param name="show_advanced" type="boolean"
				 label="Enable advanced options"
				 truevalue="show" falsevalue="">
			</param>
			<when value="show">
				<param name="allChromosomes" type="boolean" truevalue="-A" falsevalue="" checked="False"
					label="Duplicate all markers onto a single 'All Chromosomes' chromosome"
					help="Imports the data so that an additional 'All Chromosomes' chromosome is created, containing every marker in the dataset held together."/>

				<param name="collapseHets" type="boolean" truevalue="-C" falsevalue="" checked="True"
					label="Don't distinguish between heterozygous alleles"
					help="Ignores phase between heterozygous alleles, treating, for example, A/T the same as T/A."/>

				<param name="missingData" type="text" value="-"
					label="Missing data string"
					help="Alleles with missing data are encoded using this string. Clear the box to use an empty string for missing data instead."/>

				<param name="hetSep" type="text" value="/"
					label="Heterozygous allele separator string"
					help="Specifies the string used to separator heterozygous alleles (eg 'A/T'). Clear the box to specify no string is used (eg 'AT')"/>

				<param name="transposed" type="boolean" truevalue="-T" falsevalue="" checked="False"
					label="Genotype data has been transposed"
					help="Flapjack's default format has markers as columns. Select this to specify markers as rows instead."/>

				<param name="decimalEnglish" type="boolean" truevalue="-D" falsevalue="" checked="False"
					label="Force English-style decimal marks"
					help="Always process input data using '.' as the decimal separator, irrespective of this Galaxy server'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>
		<!-- WARNING: Above is the advanced options section shared by all of our tools. If you alter it here you must update the other tools as well.-->
		<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 pedigree verification of F1s (known parents) 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.

Flapjack documentation_

.. _documentation: http://flapjack.hutton.ac.uk/en/latest/command_line_support.html#pedverf1stats-exe-jhi-flapjack-io-generatepedverf1sstats
	]]></help>

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