<tool id="Tassel" name="Tassel" version="5.0">
	<description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description>
	<requirements>
                <requirement type="package" version="5.0">tassel</requirement>
        </requirements>
	<command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
#if $analysis_opts.fonction_selector == "mlm":
 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
 -fork2 -r $analysis_opts.trait
 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
  -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
 #end if
 -fork4 -k $analysis_opts.kinship
 -combineA -input1 -input2 
 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
  -input3
 #end if
 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2 
 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
  -runfork3
 #end if
 -runfork4
 
#else if $analysis_opts.fonction_selector == "glm":
 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
 -fork2 -r $analysis_opts.trait
 #if $analysis_opts.add_file.additional_file_selector == "yes":
  -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
 #end if
 -combineA -input1 -input2 
 #if $analysis_opts.add_file.additional_file_selector == "yes":
  -input3
 #end if
 -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
 #if $analysis_opts.add_file.additional_file_selector == "yes":
  -runfork3
 #end if 
#else if $analysis_opts.fonction_selector == "ld":
 -fork1 -h $hapmap
 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
#else if $analysis_opts.fonction_selector == "ck":
 -fork1 -h $hapmap
 -ck -export tmpdir$$/kinship -runfork1
#end if
	</command>
	<inputs>
		<param format="txt" name="hapmap" type="data" label="HapMap file"/>
		<conditional name="analysis_opts">
			<param name="fonction_selector" type="select" label="Type of analysis">
				<option value="mlm" selected="True">MLM</option>
				<option value="glm">GLM</option>
				<option value="ld">Linkage Disequilibrium</option>
				<option value="ck">Kinship</option>
			</param>
			<when value="glm">
                		<param format="txt" name="trait" type="data" label="Trait file"/>
				<conditional name="add_file">
					<param name="additional_file_selector" type="select" label="Add structure file">
        	                	        <option value="no" selected="True">no</option>
                	                	<option value="yes">yes</option>
	                	        </param>
					<when value="yes">
						<param format="txt" name="structure" type="data" label="Structure file"/>
					</when>
				</conditional>
			</when>
			<when value="mlm">
                		<param format="txt" name="trait" type="data" label="Trait file"/>
		                <param format="txt" name="kinship" type="data" label="Kinship file"/>
				<conditional name="add_structure_file">
					<param name="additional_file_selector" type="select" label="Add structure file">
        	                	        <option value="no" selected="True">no</option>
                	                	<option value="yes">yes</option>
	                	        </param>
					<when value="yes">
						<param format="txt" name="structure" type="data" label="Structure file"/>
					</when>
				</conditional>
				<param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
					<option value="P3D" selected="True">P3D</option>
					<option value="EachMarker">EachMarker</option>
				</param>
				<param name="mlmCompressionLevel" type="select" label="Compression Level">
					<option value="Optimum" selected="True">Optimum</option>
					<option value="Custom">Custom</option>
					<option value="None">None</option>
				</param>
                        </when>
			<when value="ld"></when>
			<when value="ck"></when>
		</conditional>
		<param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/>
	</inputs>
	<outputs>
		<data format="txt" name="output1" label="Tassel output">
			<change_format>
				<when input="analysis_opts['fonction_selector']" value="ld" format="png"/>
			</change_format>
		</data>
		
		<data format="txt" name="output2" label="Allele effects">
			<filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter>
		</data>
		
		<data format="txt" name="output3" label="Compression file">
			<filter>analysis_opts['fonction_selector'] == "mlm"</filter>
		</data>
		
		<data format="txt" name="log" label="Log file"/>
	</outputs>
	<help>

.. class:: infomark

**Program encapsulated in Galaxy by Southgreen**

.. class:: infomark

**Tassel**

-----

==========
 Authors:
==========

**Terry Casstevens**

-----

==========
 Overview
==========

Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.

-----

For further informations, please visite the website of TASSEL_.


.. _TASSEL: http://www.maizegenetics.net/tassel/

	</help>
<!--
<tests>
  <test>
      <param name="input" value="genotyping_file.inp" />
      <output name="output" file="phase_output" />
   </test>
</tests>
-->
</tool>