<tool id="Arpa" name="Arpa">

	<description>Arpa</description>
	<requirements>	
		<requirement type="package" version="1.0.0">arpa_package</requirement>
	</requirements>
	<command interpreter="ruby">
wrapper_arpa.rb $output $input
 "$tipo_script.data_type $aligner $trimmer $tipo_script.type_statistic_method.type_tree.program 
#if $tipo_script.type_statistic_method.tree_select != "bayesian":
    --bp $tipo_script.type_statistic_method.type_tree.bootstrap
#end if
#if $tipo_script.type_statistic_method.tree_select != "neighbor" and $tipo_script.type_statistic_method.tree_select != "maxparsi" and $tipo_script.type_statistic_method.type_tree.program != "-p phylip_ml":
    $tipo_script.type_statistic_method.type_tree.evolut_model --nb $tipo_script.type_statistic_method.type_tree.nb_categ 
#end if
#if $tipo_script.type_statistic_method.type_tree.program == "-p phyml":
    --a $tipo_script.type_statistic_method.type_tree.gam_distribution 
#end if
#if $tipo_script.data_type == "-t aa" and $tipo_script.type_statistic_method.type_tree.program == "-p phyml":
    --in $tipo_script.type_statistic_method.type_tree.proportion
#end if
#if $tipo_script.type_statistic_method.tree_select == "bayesian":
     --ngen $tipo_script.type_statistic_method.type_tree.ngeneration $tipo_script.type_statistic_method.type_tree.chains_run $tipo_script.type_statistic_method.type_tree.independent_analyses $tipo_script.type_statistic_method.type_tree.variation_model --printfreq $tipo_script.type_statistic_method.type_tree.chain_printed --samplefreq $tipo_script.type_statistic_method.type_tree.markov_chain --burnin $tipo_script.type_statistic_method.type_tree.samples_discarded 
#end if
#if $tipo_script.type_statistic_method.type_tree.program == "-p raxml":
    $tipo_script.type_statistic_method.type_tree.subst_rates
#end if
#if $tipo_script.data_type == "-t aa" and $tipo_script.type_statistic_method.type_tree.program == "-p raxml":
    $tipo_script.type_statistic_method.type_tree.freq_raxml_aa
#end if
#if $tipo_script.data_type == "-t nucl" and $tipo_script.type_statistic_method.type_tree.program == "-p phyml":
    --kappa $tipo_script.type_statistic_method.type_tree.trans_ratio
#end if
"
	</command>

	<inputs>

		<param name="input" type="data" format="fasta" label="Fasta file"/> 

		<param name="aligner" type="select" label="Multiple Alignment">
			<option value="-a alignm">Align-m</option>
			<option selected="True" value="-a clustalw">Clustalw</option>	
			<option value="-a mafft">Mafft</option>
			<option value="-a muscle">Muscle</option>
			<option value="-a probcons">Probcons</option>
			<option value="-a tcoffee">T-Coffee</option>
		</param>

		<param name="trimmer" type="select" label="Alignment trimming">
			<option value="-c gblocks">G Blocks</option>
			<option selected="True"  value="-c total">Total</option>
			<option value="-c trimal">TrimAl</option>
		</param>

		<conditional name="tipo_script">

			<param name="data_type" type="select" label="Select Search">
				<option value="">Select</option>
				<option value="-t aa">Amino acid sequences</option>
				<option value="-t nucl">DNA sequences</option>
			</param>

			<when value="-t aa">           

				<conditional name="type_statistic_method">

					<param name="tree_select" type="select" label="Phylogenetic tree">
						<option value="">Select</option>
						<option value="maxlike">Maximum Likelihood</option>
						<option value="neighbor">Neighbor-joining</option>
						<option value="maxparsi">Maximum Parsimony</option>
						<option value="bayesian">Bayesian Inference</option>
					</param>

					<when value="maxlike">
						<conditional name="type_tree">
							<param name="program" type="select" label="Maximum Likelihood">
								<option value="">Select</option>								
								<option value="-p phyml">PhyML</option>
								<option value="-p raxml">RAxML</option>
								<option value="-p garli">GARLI</option>
								<option value="-p phylip_ml">PHYLIP_ML</option>
								<option value="-p weighbor">WEIGHBOR</option>
							</param>

							<when value="-p phyml">
								<param name="evolut_model" type="select" label="Evolutionary model">
									<option value="--mg BLOSUM62">BLOSUM62</option>
									<option value="--mg CPREV">CPREV</option>
									<option value="--mg Dayhoff">Dayhoff</option>
									<option value="--mg DCMut">DCMut</option>
									<option value="--mg GTR">GTR</option>                           
									<option selected="True" value="--mg JTT">JTT</option>
									<option value="--mg MtMam">MtMam</option>
									<option value="--mg MtREV">MtREV</option>
									<option value="--mg RtREV">RtREV</option>
									<option value="--mg VT">VT</option>
									<option value="--mg WAG">WAG</option>                   
								</param>

								<param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>

								<param name="nb_categ" label="Substitution Rate Categories [1 - 20]" type="integer" value="4"/>

								<param name="gam_distribution" label="Gamma Distribution [1 - 20]" type="integer" value="1"/>

								<param name="proportion" label="proportion of invariable sites [0 - 20]" type="integer" value="0"/>

							</when>

							<when value="-p raxml">
								<param name="evolut_model" type="select" label="Evolutionary model">
									<option value="--mg BLOSUM62">BLOSUM62</option>
									<option value="--mg CPREV">CPREV</option>
									<option selected="True" value="--mg Dayhoff">Dayhoff</option>
									<option value="--mg DCMut">DCMut</option>
									<option value="--mg GTR">GTR</option>                           
									<option value="--mg JTT">JTT</option>
									<option value="--mg MtMam">MtMam</option>
									<option value="--mg MtREV">MtREV</option>
									<option value="--mg RtREV">RtREV</option>
									<option value="--mg VT">VT</option>
									<option value="--mg WAG">WAG</option>                   
								</param>

								<param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>

								<param name="nb_categ" label="Substitution Rate Categories [1 - 20]" type="integer" value="4"/>

								<param name="subst_rates" type="select" label="Substitution Rates">
									<option value="--rates_raxml_aa PROTGAMMA">PROTGAMMA</option>
								</param>

								<param name="freq_raxml_aa" type="select" label="Empirical Base Frequencies">
									<option value="--freq_raxml_aa F">F</option>
								</param>

							</when>


							<when value="-p garli">
								<param name="evolut_model" type="select" label="Evolutionary model">
									<option value="--mg Dayhoff">Dayhoff</option>
									<option value="--mg jones">jones</option>                           
									<option value="--mg MtMam">MtMam</option>
									<option value="--mg MtREV">MtREV</option>
									<option selected="True" value="--mg poisson">poisson</option>
									<option value="--mg WAG">WAG</option>                   
								</param>

								<param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>

								<param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>

							</when>

							<when value="-p phylip_ml">
								<param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
							</when>


							<when value="-p weighbor">
								<param name="evolut_model" type="select" label="Evolutionary model">
									<option value="--mg BLOSUM62">BLOSUM62</option>
									<option value="--mg Dayhoff">Dayhoff</option>                           
									<option value="--mg JTT">JTT</option>
									<option value="--mg MTREV24">MTREV24</option>
									<option value="--mg VT">VT</option>
									<option selected="True" value="--mg WAG">WAG</option>                   
								</param>

								<param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>

								<param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="6"/>

							</when>

						</conditional>

					</when>


					<when value="neighbor">
						<conditional name="type_tree">
							<param name="program" type="select" label="Neighbor-joining">
								<option selected="True" value="-p phylip_nj">PHYLIP_NJ</option>
							</param>

							<when value="-p phylip_nj">
								<param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
							</when>

						</conditional>
					</when>

					<when value="maxparsi">
						<conditional name="type_tree">
							<param name="program" type="select" label="Maximum Parsimony">
								<option selected="True" value="-p phylip_mp">PHYLIP_MP</option>
							</param>

							<when value="-p phylip_mp">
								<param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="500"/>
							</when>

						</conditional>
					</when>

					<when value="bayesian">
						<conditional name="type_tree">
							<param name="program" type="select" label="Bayesian Inference">
								<option value="-p mrbayes">MrBayes</option>
							</param>

							<when value="-p mrbayes">
								<param name="evolut_model" type="select" label="Evolutionary model">
									<option value="--mg BLOSUM">BLOSUM</option>
									<option value="--mg CPREV">CPREV</option>
									<option value="--mg Dayhoff">Dayhoff</option>
									<option value="--mg equalin">equalin</option>
									<option value="--mg GTR">GTR</option>                           
									<option value="--mg jones">jones</option>
									<option value="--mg MtMam">MtMam</option>
									<option value="--mg MtREV">MtREV</option>
									<option selected="True" value="--mg poisson">poisson</option>
									<option value="--mg RtREV">RtREV</option>
									<option value="--mg VT">VT</option>
									<option value="--mg WAG">WAG</option>                   
								</param>

								<param name="ngeneration" label="Generation Number[10 - 1000000]" type="integer" value="1000"/>

								<param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>

								<param name="chain_printed" label="Chain Printed[1 - 1000]" type="integer" value="100"/>

								<param name="markov_chain" label="Markov Chain Sampled[1 - 1000]" type="integer" value="100"/>

								<param name="chains_run" type="select" label="Chains Run">
									<option value="--nchains 0">0</option>
									<option value="--nchains 1">1</option>
									<option value="--nchains 2">2</option>
									<option value="--nchains 3">3</option>
									<option selected="True" value="--nchains 4">4</option>
								</param>

								<param name="samples_discarded" label="Number of Samples Discarded[10 - 1000]" type="integer" value="10"/>

								<param name="independent_analyses" type="select" label="Number of independent Analyses">
									<option selected="True" value="--nruns 2">2</option>
								</param>

								<param name="variation_model" type="select" label="Rate Variation Model">
									<option selected="True" value="--rates_mrbayes Equal">Equal</option>
								</param>
							</when>
						</conditional>
					</when>
				</conditional>
			</when>



			<when value="-t nucl">           

				<conditional name="type_statistic_method">
					<param name="tree_select" type="select" label="Phylogenetic tree">
						<option value="">Select</option>
						<option value="maxlike">Maximum Likelihood</option>
						<option value="neighbor">Neighbor-joining</option>
						<option value="maxparsi">Maximum Parsimony</option>
						<option value="bayesian">Bayesian Inference</option>
					</param>
					<when value="maxlike">
						<conditional name="type_tree">

							<param name="program" type="select" label="Maximum Likelihood">
								<option value="">Select</option>								
								<option value="-p phyml">PhyML</option>
								<option value="-p raxml">RAxML</option>
								<option value="-p garli">GARLI</option>
								<option value="-p phylip_ml">PHYLIP_ML</option>
								<option value="-p weighbor">WEIGHBOR</option>
							</param>

							<when value="-p phyml">
								<param name="evolut_model" type="select" label="Evolutionary model">
									<option value="--mg Custom">Custom</option>
									<option value="--mg F81">F81</option>
									<option value="--mg F84">F84</option>
									<option value="--mg GTR">GTR</option>
									<option selected="True" value="--mg HKY">HKY</option>                           
									<option value="--mg JC69">JC69</option>
									<option value="--mg K2P">K2P</option>
									<option value="--mg TN93">TN93</option>                   
								</param>

								<param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>

								<param name="nb_categ" label="Substitution Rate Categories [1 - 20]" type="integer" value="4"/>

								<param name="gam_distribution" label="Gamma Distribution [1 - 20]" type="integer" value="1"/>

								<param name="trans_ratio" label="Transition / transversion ratio [0 - 20]" type="integer" value="4"/>

							</when>

							<when value="-p raxml">
								<param name="evolut_model" type="select" label="Evolutionary model">
									<option selected="True" value="--mg GTR">GTR</option>                                               
								</param>

								<param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>

								<param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>

								<param name="subst_rates" type="select" label="Substitution Rates">
									<option selected="True" value="--rates_raxml_nucl GAMMA">GAMMA</option>
								</param>

							</when>


							<when value="-p garli">
								<param name="evolut_model" type="select" label="Evolutionary model">
									<option value="--mg F81">F81</option>
									<option value="--mg GTR">GTR</option>
									<option value="--mg HKY">HKY</option>                           
									<option selected="True" value="--mg JC">JC</option>
									<option value="--mg K3P">K3P</option>
									<option value="--mg K80">K80</option>
									<option value="--mg SYM">SYM</option>
									<option value="--mg TIM">TIM</option>
									<option value="--mg TrN">TrN</option>
									<option value="--mg TVM">TVM</option>                   
								</param>

								<param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>

								<param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>

							</when>

							<when value="-p phylip_ml">
								<param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
							</when>


							<when value="-p weighbor">
								<param name="evolut_model" type="select" label="Evolutionary model">
									<option value="--mg GTR">GTR</option>
									<option selected="True" value="--mg HKY">HKY</option>                           
									<option value="--mg TN">TN</option>
								</param>

								<param name="bootstrap" label="bootstrap [10 - 1000]" type="integer" value="100"/>

								<param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>

							</when>

						</conditional>
					</when>


					<when value="neighbor">
						<conditional name="type_tree">
							<param name="program" type="select" label="Neighbor-joining">
								<option selected="True" value="-p phylip_nj">PHYLIP_NJ</option>
							</param>

							<when value="-p phylip_nj">
								<param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="100"/>
							</when>

						</conditional>
					</when>

					<when value="maxparsi">
						<conditional name="type_tree">
							<param name="program" type="select" label="Maximum Parsimony">
								<option selected="True" value="-p phylip_mp">PHYLIP_MP</option>
							</param>

							<when value="-p phylip_mp">
								<param name="bootstrap" label="Bootstrap [10 - 10000]" type="integer" value="500"/>
							</when>

						</conditional>
					</when>

					<when value="bayesian">
						<conditional name="type_tree">
							<param name="program" type="select" label="Bayesian Inference">
								<option selected="True" value="-p mrbayes">MrBayes</option>
							</param>

							<when value="-p mrbayes">
								<param name="evolut_model" type="select" label="Evolutionary model">
									<option value="--mg F81">F81</option>
									<option value="--mg GTR">GTR</option>
									<option value="--mg HKY">HKY</option>
									<option value="--mg HKY85">HKY85</option>
									<option selected="--mg True" value="JC">JC</option>                           
									<option value="--mg JC69">JC69</option>
									<option value="--mg K3P">K3P</option>
									<option value="--mg K80">K80</option>
									<option value="--mg SYM">SYM</option>
									<option value="--mg TIM">TIM</option>
									<option value="--mg TrN">TrN</option>
									<option value="--mg TVM">TVM</option>                   
								</param>

								<param name="ngeneration" label="Generation Number[10 - 1000000]" type="integer" value="1000"/>

								<param name="nb_categ" label="Substitution Rate Categories [0 - 20]" type="integer" value="4"/>

								<param name="chain_printed" label="Chain Printed[1 - 1000]" type="integer" value="100"/>

								<param name="markov_chain" label="Markov Chain Sampled[1 - 1000]" type="integer" value="100"/>

								<param name="chains_run" type="select" label="Chains Run:">
									<option selected="True" value="--nchains 4">4</option>
								</param>

								<param name="samples_discarded" label="Number of Samples Discarded[0 - 20]" type="integer" value="10"/>

								<param name="independent_analyses" type="select" label="Number of independent Analyses">
									<option selected="True" value="--nruns 2">2</option>
								</param>

								<param name="variation_model" type="select" label="Rate Variation Model">
									<option selected="True" value="--rates_mrbayes Equal">Equal</option>
								</param>
							</when>
						</conditional>
					</when>
				</conditional>

			</when>

		</conditional>       
	</inputs>

	<outputs>
		<data format="txt" name="output" />
	</outputs>

	<tests>
		<test>
			<param name="input" value=""/>
			<output name="out_file1" file=""/>
		</test>
	</tests>

	<help>
	</help>

</tool>