<tool id="Tassel" name="Tassel" version="3.0.0">
	<description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
	<requirements>
				<requirement type="package" version="5.2.89">tassel</requirement>
        </requirements>
    <stdio>
        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
        <exit_code range="1:" level="fatal" />
    </stdio>
    <command>
#if $analysis_opts.fonction_selector == "ck":
 mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1;
#else if $analysis_opts.fonction_selector == "ld":
 mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1;
#else if $analysis_opts.fonction_selector == "glm":
 #if $analysis_opts.add_file.additional_file_selector == "no":
  mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -combineA -input1 -input2 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2;
 #else if $analysis_opts.add_file.additional_file_selector == "yes":
  mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait -combineA -input1 -input2 -input3 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 -runfork3 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2;
 #end if
#else if $analysis_opts.fonction_selector == "mlm":
 #if $analysis_opts.add_structure_file.additional_file_selector == "no": 
  mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork4 >>$log;mv tmpdir$$/output2.txt $output1;mv tmpdir$$/output3.txt $output2;mv tmpdir$$/output4.txt $output3;
 #else if $analysis_opts.add_structure_file.additional_file_selector == "yes":
  mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -input3 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork3 -runfork4 >>$log;mv tmpdir$$/output2.txt $output1;mv tmpdir$$/output3.txt $output2;mv tmpdir$$/output4.txt $output3;
 #end if
#end if
	</command>
	<inputs>
		<param format="vcf" name="vcffile" type="data" label="VCF 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>
                                        <when value="no">
                                        </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>
                                        <when value="no">
                                        </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>
    <tests>
        <test>
            <param name="vcffile" value="input.vcf"/>
            <conditional name="analysis_opts">
                <param name="fonction_selector" value="glm"/>
                <param name="trait" value="phenotyping_xantho.tsv"/>
                <conditional name="add_structure_file">
                    <param name="additional_file_selector" value="yes"/>
                    <param name="structure" value="Best_K_Output2"/>
                </conditional>
            </conditional>
            <param name="filterAlignMinFreq" value="0.05"/>
            <output name="output1" value="statistics_output.txt"/>
            <output name="output2" value="Allele_effects_output.txt"/>
        </test>
    </tests>
    <help><![CDATA[
	    .. class:: infomark

	    **Tassel5** version 5.2.40

	    .. class:: infomark

	    **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)

	    .. class:: infomark

	    **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr

	    ---------------------------------------------------

	    =======
	    Tassel5
	    =======

	    -----------
	    Description
	    -----------

	    | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
	    | For further informations on tassel, please visit the website_.

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

	    ------------
	    Dependencies
	    ------------

	    Tassel5

	    tassel_ 5.2.40, Conda version

	    .. _tassel: https://anaconda.org/bioconda/tassel

    ]]></help>
    <citations>
       <citation type="doi">10.1093/bioinformatics/btm308</citation>
    </citations>
</tool>