Mercurial > repos > biowebdb > arpa
diff wrapper_arpa.xml @ 0:7548aa64d696 draft
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| author | biowebdb |
|---|---|
| date | Wed, 03 Feb 2016 11:22:53 -0500 |
| parents | |
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--- /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>