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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 6e1b47bf8f06b9d92b369c2f36e52f4fc451d39c
| author | iuc |
|---|---|
| date | Thu, 21 Jul 2022 15:16:20 +0000 |
| parents | 73a469f7dc96 |
| children | ea30d3089354 |
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<tool id="raxml" name="Phyogenetic reconstruction with RAxML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>- Maximum Likelihood based inference of large phylogenetic trees</description> <macros> <token name="@TOOL_VERSION@">8.2.4</token> <token name="@VERSION_SUFFIX@">3</token> </macros> <xrefs> <xref type="bio.tools">raxml</xref> </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">raxml</requirement> <requirement type="package" version="3.6">python</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1 slots=\${GALAXY_SLOTS:-1}; if [ "\$slots" == "1" ]; then bin="raxmlHPC"; else bin="raxmlHPC-PTHREADS -T \$slots"; fi; \$bin -s '$infile' -n galaxy #if $search_model_selector.model_type == 'aminoacid': -m ${search_model_selector.base_model}${search_model_selector.aa_search_matrix}${search_model_selector.aa_model_empirical_base_frequencies} #else: -m $search_model_selector.base_model #end if -p $random_seed #if $selExtraOpts.extraOptions == 'full': #if $selExtraOpts.number_of_runs_conditional.number_of_runs_selector == 'by_number_of_runs': -N $selExtraOpts.number_of_runs_conditional.number_of_runs #else: -N $selExtraOpts.number_of_runs_conditional.number_of_runs_bootstop #end if #if $selExtraOpts.weightfile: -a '$selExtraOpts.weightfile' #end if #if $selExtraOpts.secondary_structure_model: -A $selExtraOpts.secondary_structure_model #end if #if str($selExtraOpts.bootseed): -b $selExtraOpts.bootseed #end if -B $selExtraOpts.cutoff_threshold -c $selExtraOpts.numofcats $selExtraOpts.search_complete_random_tree $selExtraOpts.ml_search_convergence #if $selExtraOpts.model_opt_precision: -e $selExtraOpts.model_opt_precision #end if #if $selExtraOpts.excludefile: -E '$selExtraOpts.excludefile' #end if #if $selExtraOpts.search_algorithm: -f $selExtraOpts.search_algorithm #end if $selExtraOpts.save_memory_cat_model #if $selExtraOpts.groupingfile: -g '$selExtraOpts.groupingfile' #end if #if $selExtraOpts.enable_evol_heuristics: -G $selExtraOpts.enable_evol_heuristics #end if #if str($selExtraOpts.initial_rearrangement_setting): -i $selExtraOpts.initial_rearrangement_setting #end if #if $selExtraOpts.posterior_bootstopping_analysis: -I $selExtraOpts.posterior_bootstopping_analysis #end if #if $selExtraOpts.majority_rule_consensus: -J $selExtraOpts.majority_rule_consensus #end if $selExtraOpts.print_branch_lengths -K $selExtraOpts.multistate_sub_model $selExtraOpts.estimate_individual_branch_lengths #if $selExtraOpts.outgroup_name: -o '$selExtraOpts.outgroup_name' #end if $selExtraOpts.disable_undetermined_seq_check #if $selExtraOpts.external_protein_model: -P '$selExtraOpts.external_protein_model' #end if #if $selExtraOpts.multiple_model: -q '$selExtraOpts.multiple_model' #end if #if $selExtraOpts.constraint_file: -r '$selExtraOpts.constraint_file' #end if #if $selExtraOpts.bin_model_parameter_file: -R '$selExtraOpts.bin_model_parameter_file' #end if #if $selExtraOpts.secondary_structure_file: -S '$selExtraOpts.secondary_structure_file' #end if #if $selExtraOpts.start_tree_file: -t '$selExtraOpts.start_tree_file' #end if $selExtraOpts.use_median_approximation $selExtraOpts.save_memory_gappy_alignments $selExtraOpts.disable_rate_heterogeneity -W $selExtraOpts.sliding_window_size #if str($selExtraOpts.rapid_bootstrap_random_seed): -x $selExtraOpts.rapid_bootstrap_random_seed #end if $selExtraOpts.parsimony_starting_tree_only #end if && python '$__tool_directory__/raxml.py' #if $selExtraOpts.extraOptions == 'full': #if str($selExtraOpts.bootseed): --bootseed $selExtraOpts.bootseed #end if #if str($selExtraOpts.rapid_bootstrap_random_seed): --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed #end if #if $selExtraOpts.number_of_runs_conditional.number_of_runs_selector == 'by_number_of_runs': --number_of_runs $selExtraOpts.number_of_runs_conditional.number_of_runs #end if #if $selExtraOpts.multiple_model: --multiple_model '$selExtraOpts.multiple_model' #end if #end if ]]></command> <inputs> <param name="infile" argument="-s" type="data" format="fasta,phylip" label="Source file with aligned sequences" help="At least four aligned genomes are needed for RAxML." /> <conditional name="search_model_selector"> <param name="model_type" type="select" label="Model type"> <option value="nucleotide" selected="true">Nucleotide</option> <option value="aminoacid">Amino Acid</option> <option value="binary">Binary</option> <option value="multistate">Multistate</option> </param> <when value="nucleotide"> <param name="base_model" type="select" label="Substitution model"> <option value="GTRCAT">GTRCAT</option> <option value="GTRCATI">GTRCATI</option> <option value="GTRGAMMA" selected="true">GTRGAMMA</option> <option value="GTRGAMMAI">GTRGAMMAI</option> </param> </when> <when value="aminoacid"> <param name="base_model" type="select" label="Substitution model"> <option value="PROTCAT" selected="true">PROTCAT</option> <option value="PROTCATI">PROTCATI</option> <option value="PROTGAMMA">PROTGAMMA</option> <option value="PROTGAMMAI">PROTGAMMAI</option> </param> <param name="aa_search_matrix" type="select" label="Matrix"> <option value="DAYHOFF" selected="true">DAYHOFF</option> <option value="DCMUT">DCMUT</option> <option value="JTT">JTT</option> <option value="MTREV">MTREV</option> <option value="WAG">WAG</option> <option value="RTREV">RTREV</option> <option value="CPREV">CPREV</option> <option value="VT">VT</option> <option value="BLOSUM62">BLOSUM62</option> <option value="MTMAM">MTMAM</option> <option value="LG">LG</option> <option value="MTART">MTART</option> <option value="MTZOA">MTZOA</option> <option value="PMB">PMB</option> <option value="HIVB">HIVB</option> <option value="HIVW">HIVW</option> <option value="JTTDCMUT">JTTDCMUT</option> <option value="FLU">FLU</option> <option value="DUMMY">DUMMY</option> <option value="DUMMY2">DUMMY2</option> <option value="GTR_UNLINKED">GTR_UNLINKED</option> <option value="GTR">GTR</option> </param> <param name="aa_model_empirical_base_frequencies" type="boolean" truevalue="F" falsevalue="" checked="no" display="checkboxes" label="Use empirical base frequencies in AA models" /> </when> <when value="binary"> <param name="base_model" type="select" label="Substitution model"> <option value="BINCAT">BINCAT</option> <option value="BINCATI">BINCATI</option> <option value="BINGAMMA">BINGAMMA</option> <option value="BINGAMMAI">BINGAMMAI</option> </param> </when> <when value="multistate"> <param name="base_model" type="select" label="Substitution model"> <option value="MULTICAT">MULTICAT</option> <option value="MULTICATI">MULTICATI</option> <option value="MULTIGAMMA">MULTIGAMMA</option> <option value="MULTIGAMMAI">MULTIGAMMAI</option> </param> </when> </conditional> <param name="random_seed" argument="-p" type="integer" value="1234567890" label="Random seed used for the parsimony inferences" /> <conditional name="selExtraOpts"> <param name="extraOptions" type="select" label="RAxML options to use" help="The required minimal settings are the input file and the substitution model. To specify extra options select the 'Full option list'"> <option value="required">Required options only</option> <option value="full">Full option list</option> </param> <when value="required" /> <when value="full"> <conditional name="number_of_runs_conditional"> <param name="number_of_runs_selector" type="select" label="Multiple boostrap specification"> <option value="by_number_of_runs">By number of runs</option> <option value="by_bootstopping">By bootstopping criteria</option> </param> <when value="by_number_of_runs"> <param name="number_of_runs" argument="-N" type="integer" value="1" label="Number of alternative runs on distinct starting trees" help="In combination with the '-b' option, this will invoke a multiple boostrap analysis" /> </when> <when value="by_bootstopping"> <param name="number_of_runs_bootstop" argument="-N" type="select" label="Bootstopping criteria" help="Bootstopping will only work in combination with '-x' or '-b'"> <option value="autoMR">autoMR</option> <option value="autoMRE">autoMRE</option> <option value="autoMRE_IGN">autoMRE_IGN</option> <option value="autoFC">autoFC</option> </param> </when> </conditional> <param name="weightfile" argument="-a" type="data" format="txt" optional="true" label="Column weight file" /> <param name="secondary_structure_model" argument="-A" type="select" optional="true" label="Secondary structure substitution model"> <option value="S6A">S6A</option> <option value="S6B">S6B</option> <option value="S6C">S6C</option> <option value="S6D">S6D</option> <option value="S6E">S6E</option> <option value="S7A">S7A</option> <option value="S7B">S7B</option> <option value="S7C">S7C</option> <option value="S7D">S7D</option> <option value="S7E">S7E</option> <option value="S7F">S7F</option> <option value="S16">S16</option> <option value="S16A">S16A</option> <option value="S16B">S16B</option> </param> <param name="bootseed" argument="-b" type="integer" value="" optional="true" label="Random seed for non-parametric bootstrapping" help="Specifying a value turns on bootstrapping" /> <param name="rapid_bootstrap_random_seed" argument="-x" type="integer" value="" optional="true" label="Random seed for rapid bootstrapping" help="Specifying a value turns on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT" /> <param name="cutoff_threshold" argument="-B" type="float" value="0.03" min="0" max="1" label="MR cutoff threshold" help="Cutoff threshold for the MR-based bootstopping criteria" /> <param name="numofcats" argument="-c" type="integer" value="25" label="Number of Rate Categories for GTRCAT/GTRMIX" /> <!-- (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now. --> <param name="search_complete_random_tree" argument="-d" type="boolean" truevalue="-d" falsevalue="" label="Start ML optimization from a complete random starting tree" /> <param name="ml_search_convergence" argument="-D" type="boolean" truevalue="-D" falsevalue="" label="ML search convergence criterion" help="This will break off ML searches if the relative Robinson-Foulds distance between the trees obtained from two consecutive lazy SPR cycles is smaller or equal to 1%. Usage recommended for very large datasets in terms of taxa. On trees with more than 500 taxa this will yield execution time improvements of approximately 50% while yielding only slightly worse trees" /> <param name="model_opt_precision" argument="-e" type="float" label="Model optimization precision" value="" optional="true" help="Set model optimization precision in log likelihood units for final optimization of tree topology" /> <param name="excludefile" argument="-E" type="data" format="txt" optional="true" label="Exclude file" help="Should contain a specification of alignment positions you wish to exclude" /> <param name="search_algorithm" argument="-f" type="select" label="Algorithm to execute" optional="true"> <option value="a">Rapid bootstrap and best ML tree search (a)</option> <option value="A">Compute marginal ancestral states (A)</option> <option value="b">Draw bipartition information (b)</option> <option value="c">Check if the alignment can be read (c)</option> <option value="d" selected="true">New rapid hill-climbing (d)</option> <option value="D">Rapid hill-climbing with RELL bootstraps (D)</option> <option value="e">Optimize model+branch lengths under GAMMA/GAMMAI only (e)</option> <option value="g">Compute per-site log likelihoods for -z trees (g)</option> <option value="h">Compute log likelihood test for -t / -z trees (h)</option> <option value="j">Generate bootstrapped alignment files (j)</option> <option value="J">Compute SH-like support values for the -t tree (J)</option> <option value="m">Compare bipartitions between -t and -z trees (m)</option> <option value="n">Compute log likelihood score for -z trees (n)</option> <option value="o">Use old slower search algorithm (o)</option> <option value="p">Stepwise MP addition of new sequences (p)</option> <option value="q">Fast quartet calculator (q)</option> <option value="r">Compute pairwise RF distances in -z trees (r)</option> <option value="s">Split a multi-gene alignment (s)</option> <option value="S">Compute site-specific placement bias (S)</option> <option value="t">Randomized tree searches on a fixed starting tree (t)</option> <option value="T">Final optimization of a ML tree from a bootstrap (T)</option> <option value="u">Morphological weight calibration using ML on a -t tree (u)</option> <option value="v">Classify environmental sequences (v)</option> <option value="w">Compute ELW-test on -z trees (w)</option> <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option> <option value="y">Classify environmental sequences into a reference tree (y)</option> </param> <param name="save_memory_cat_model" argument="-F" type="boolean" truevalue="-F" falsevalue="" label="ML tree searches under CAT model" help="ML tree searches under CAT model for very large trees without switching to GAMMA in the end (saves memory) and no thorough optimization under GAMMA" /> <param name="groupingfile" argument="-g" type="data" format="txt" optional="true" label="Multifurcating constraint tree" help="This tree does not need to be comprehensive, i.e. does not have to contain all taxa" /> <param name="enable_evol_heuristics" argument="-G" type="float" min="0.0" max="1.0" optional="true" label="Enable the ML-based evolutionary placement algorithm heuristics" help="By specifying a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML)" /> <param name="initial_rearrangement_setting" argument="-i" type="integer" value="" optional="true" label="Initial rearrangement setting for the subsequent application of topological changes phase" /> <param name="posterior_bootstopping_analysis" argument="-I" type="select" optional="true" label="A posteriori bootstopping analysis"> <option value="autoFC">Frequency-based criterion (autoFC)</option> <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option> <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option> <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option> </param> <!-- (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy --> <param name="majority_rule_consensus" argument="-J" type="select" optional="true" label="Compute consensus tree"> <option value="MR">Majority-rule consensus tree (MR)</option> <option value="MRE">Extended majority-rule consensus tree (MRE)</option> <option value="STRICT">Strict consensus tree (STRICT)</option> <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option> <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option> </param> <param name="print_branch_lengths" argument="-k" type="boolean" truevalue="-k" falsevalue="" label="Print bootstrapped trees with branch lengths" help="The bootstraps will run a bit longer, because model parameters will be optimized at the end of each run under GAMMA or GAMMA+P-Invar respectively" /> <param name="multistate_sub_model" argument="-K" type="select" label="Specify a multi-state substitution model"> <option value="GTR" selected="true">GTR</option> <option value="ORDERED">ORDERED</option> <option value="MK">MK</option> </param> <param name="estimate_individual_branch_lengths" argument="-M" type="boolean" truevalue="-M" falsevalue="" label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file. A weighted average of the branch lengths is computed by using the respective partition lengths" /> <param name="outgroup_name" argument="-o" type="text" value="" optional="true" label="Outgroup name" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed" /> <param name="disable_undetermined_seq_check" argument="-O" type="boolean" truevalue="-O" falsevalue="" label="Disable check for completely undetermined sequence in alignment" help="The program will not exit with an error message when '-O' is specified." /> <param name="external_protein_model" argument="-P" type="data" format="txt" optional="true" label="External AA (Protein) substitution model" help="This file must contain 420 entries, the first 400 being the AA substitution rates (this must be a symmetric matrix) and the last 20 are the empirical base frequencies" /> <param name="multiple_model" argument="-q" type="data" format="txt" optional="true" label="Assignment of models to alignment partitions for multiple models of substitution" help="For the syntax of this file please consult the RaXML manual" /> <param name="constraint_file" argument="-r" type="data" format="txt" optional="true" label="Binary constraint tree" help="This tree does not need to be comprehensive, i.e. does not have to contain all taxa" /> <param name="bin_model_parameter_file" argument="-R" type="data" format="txt" optional="true" label="Binary model parameter file" help="This parameter file can be generated with RAxML using the '-f e' tree evaluation option" /> <param name="secondary_structure_file" argument="-S" type="data" format="txt" optional="true" label="Secondary structure file" help="The file can contain '.' for alignment columns that do not form part of a stem and characters '()<>[]{}' to define stem regions and pseudoknots" /> <param name="start_tree_file" argument="-t" type="data" format="nhx" optional="true" label="Starting tree file" help="In Newick format" /> <param name="use_median_approximation" argument="-u" type="boolean" truevalue="-u" falsevalue="" label="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity" /> <param name="save_memory_gappy_alignments" argument="-U" type="boolean" truevalue="-U" falsevalue="" label="Save memory on large gappy alignments" help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments. This will only work for DNA and/or PROTEIN data" /> <param name="disable_rate_heterogeneity" argument="-V" type="boolean" truevalue="-V" falsevalue="" label="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead" help="Only works if you specify the CAT model of rate heterogeneity" /> <param name="sliding_window_size" argument="-W" type="integer" min="1" value="100" label="Sliding window size for leave-one-out site-specific placement bias algorithm" help="Only effective when used in combination with '-f S'" /> <param name="parsimony_starting_tree_only" argument="-y" type="boolean" truevalue="-y" falsevalue="" label="Compute a randomized parsimony starting tree only" help="The program will exit after computation of the starting tree" /> </when> </conditional> </inputs> <outputs> <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" /> <!-- REQUIRED --> <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log"> <filter>selExtraOpts['extraOptions'] == 'required'</filter> <filter>selExtraOpts['search_algorithm'] != 'a'</filter> </data> <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> <filter>selExtraOpts['extraOptions'] == 'required'</filter> <filter>selExtraOpts['search_algorithm'] != 'a'</filter> </data> <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result"> <filter>selExtraOpts['extraOptions'] == 'required'</filter> <filter>selExtraOpts['search_algorithm'] != 'a'</filter> </data> <!-- ADVANCED --> <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree"> <filter>selExtraOpts['search_complete_random_tree'] is True</filter> <filter>selExtraOpts['extraOptions'] == "full"</filter> </data> <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> <!-- <filter>selExtraOpts['extraOptions'] == 'full'</filter> --> <!-- <filter>selExtraOpts['search_algorithm'] != 'b'</filter> <filter>not selExtraOpts['majority_rule_consensus']</filter> --> </data> <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['multiple_model'] != ''</filter> </data> <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['multiple_model'] is not None </filter> </data> <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter> <filter>selExtraOpts['bootseed'] == ''</filter> <filter>selExtraOpts['search_algorithm'] != 'a'</filter> <filter>selExtraOpts['search_algorithm'] != 'b'</filter> <filter>not selExtraOpts['majority_rule_consensus']</filter> </data> <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter> <filter>selExtraOpts['bootseed'] == ''</filter> <filter>selExtraOpts['search_algorithm'] != 'a'</filter> <filter>selExtraOpts['search_algorithm'] != 'b'</filter> <filter>not selExtraOpts['majority_rule_consensus']</filter> </data> <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['multiple_model'] is not None</filter> </data> <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <!-- <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter> <filter>selExtraOpts['bootseed'] == ''</filter> <filter>selExtraOpts['search_algorithm'] != 'a'</filter> <filter>selExtraOpts['constraint_file'] is None</filter> <filter>selExtraOpts['groupingfile'] is None</filter> <filter>selExtraOpts['search_complete_random_tree'] is False</filter> <filter>selExtraOpts['start_tree_file'] is None</filter> <filter>not selExtraOpts['majority_rule_consensus'] == ''</filter> --> </data> <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter> <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter> </data> <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions"> <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter> <filter>selExtraOpts['extraOptions'] == "full"</filter> </data> <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter> </data> <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['majority_rule_consensus'] == 'STRICT'</filter> </data> <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['majority_rule_consensus'] == 'MR'</filter> </data> <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree"> <filter>selExtraOpts['extraOptions'] == "full"</filter> <filter>selExtraOpts['majority_rule_consensus'] == 'MRE'</filter> </data> <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences."> <filter>selExtraOpts['search_algorithm'] == 'm' </filter> <filter>selExtraOpts['extraOptions'] == "full"</filter> </data> <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores"> <filter>selExtraOpts['search_algorithm'] == 'g' </filter> <filter>selExtraOpts['extraOptions'] == "full"</filter> </data> <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances"> <filter>selExtraOpts['search_algorithm'] == 'x' </filter> <filter>selExtraOpts['extraOptions'] == "full"</filter> </data> </outputs> <tests> <test> <param name="extraOptions" value="required"/> <param name="infile" value="dna.phy"/> <param name="model_type" value="nucleotide"/> <param name="base_model" value="GTRCAT"/> <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" /> <output name="bestTree" ftype="nhx"> <assert_contents> <has_text_matching expression="Frog" /> </assert_contents> </output> </test> <test> <param name="extraOptions" value="full"/> <param name="infile" value="dna.fasta"/> <param name="model_type" value="nucleotide"/> <param name="base_model" value="GTRCAT"/> <param name="number_of_runs" value="5"/> <output name="parsimonyTree" ftype="nhx"> <assert_contents> <has_text_matching expression="Chicken" /> </assert_contents> </output> <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" ftype="nhx" compare="re_match"/> <output name="bestTree" ftype="nhx"> <assert_contents> <has_text_matching expression="Whale" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ RAxML_ (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic trees. The program is explicitly being developed to efficiently infer trees for extremely large datasets, either in terms of the number of taxa and/or the sequence length. .. _RAxML: http://www.exelixis-lab.org/web/software/raxml/ **Tool development**: Oleksandr Moskalenko with adaptations from Tiago Antao. ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btu033</citation> </citations> </tool>