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changeset 0:7548aa64d696 draft

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Uploaded
author biowebdb
date Wed, 03 Feb 2016 11:22:53 -0500
parents
children 2b93b36547ba
files wrapper_arpa.xml
diffstat 1 files changed, 460 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wrapper_arpa.xml	Wed Feb 03 11:22:53 2016 -0500
@@ -0,0 +1,460 @@
+<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>