# HG changeset patch # User biowebdb # Date 1454516573 18000 # Node ID 7548aa64d6960b64dbd8bf1edb2cb6a6700e310e Uploaded diff -r 000000000000 -r 7548aa64d696 wrapper_arpa.xml --- /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 @@ + + + Arpa + + arpa_package + + +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 +" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +