Mercurial > repos > iuc > raxml
diff raxml.xml @ 0:6805e85573b8 draft
planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
| author | iuc |
|---|---|
| date | Mon, 14 Nov 2016 14:03:39 -0500 |
| parents | |
| children | ba29b5e2a4be |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/raxml.xml Mon Nov 14 14:03:39 2016 -0500 @@ -0,0 +1,545 @@ +<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.2"> + <description>- Maximum Likelihood based inference of large phylogenetic trees</description> + <requirements> + <requirement type='package' version="8.2.4">raxml</requirement> + </requirements> + <command interpreter="python">raxml.py + ## Required parameters + ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1 + ## (-T) + ## Cannot have --threads 1 + #set $slots = $getVar('GALAXY_SLOTS', 1) + #if $slots == 1: + --binary "raxmlHPC" + --threads 1 + #else: + --binary "raxmlHPC-PTHREADS" + --threads $slots + #end if + ## (-s) + --source "$infile" + ## (-m) + --model_type $search_model_selector.model_type + --base_model $search_model_selector.base_model + #if str( $search_model_selector.model_type ) == 'aminoacid': + $search_model_selector.aa_model_empirical_base_frequencies + #if $search_model_selector.aa_search_matrix: + --aa_search_matrix $search_model_selector.aa_search_matrix + #end if + #end if + + ## Optional parameters + + #if str( $selExtraOpts.extraOptions ) == 'full': + ## (-N/#) + #if $selExtraOpts.number_of_runs: + --number_of_runs $selExtraOpts.number_of_runs + #end if + #if $selExtraOpts.number_of_runs_bootstop: + --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop + #end if + ## (-a) + #if $selExtraOpts.weightfile: + --weightfile "$selExtraOpts.weightfile" + #end if + ## (-b) + #if str ($selExtraOpts.secondary_structure_model) != "": + --secondary_structure_model $selExtraOpts.secondary_structure_model + #end if + ## (-b) + #if str($selExtraOpts.bootseed): + --bootseed $selExtraOpts.bootseed + #end if + ## (-c) + #if $selExtraOpts.numofcats: + --numofcats $selExtraOpts.numofcats + #end if + ## (-d) + $selExtraOpts.search_complete_random_tree + ## (-D) + $selExtraOpts.ml_search_convergence + ## (-e) + #if $selExtraOpts.model_opt_precision: + --model_opt_precision $selExtraOpts.model_opt_precision + #end if + ## (-E) + #if $selExtraOpts.excludefile: + --excludefile "$selExtraOpts.excludefile" + #end if + ## (-f) + #if $selExtraOpts.search_algorithm: + --search_algorithm $selExtraOpts.search_algorithm + #end if + ## (-F) + $selExtraOpts.save_memory_cat_model + ## (-g) + #if $selExtraOpts.groupingfile: + --groupingfile "$selExtraOpts.groupingfile" + #end if + ## (-G) + #if $selExtraOpts.enable_evol_heuristics: + --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics + #end if + ## (-i) + #if $selExtraOpts.initial_rearrangement_setting: + --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting + #end if + ## (-I) + #if $selExtraOpts.posterior_bootstopping_analysis: + --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis + #end if + ## (-J) + #if $selExtraOpts.majority_rule_consensus: + --majority_rule_consensus $selExtraOpts.majority_rule_consensus + #end if + ## (-k) + $selExtraOpts.print_branch_lengths + ## (-K) + #if str ($selExtraOpts.multistate_sub_model) != "": + --multistate_sub_model $selExtraOpts.multistate_sub_model + #end if + ## (-m) - see elsewhere + ## (-M) + $selExtraOpts.estimate_individual_branch_lengths + ## (-n) - see elsewhere + ## (-o) + #if $selExtraOpts.outgroup_name: + --outgroup_name "$selExtraOpts.outgroup_name" + #end if + ## (-O) + $selExtraOpts.disable_undetermined_seq_check + ## (-P) + #if $selExtraOpts.external_protein_model: + --external_protein_model "$selExtraOpts.external_protein_model" + #end if + ## (-q) + #if $selExtraOpts.multiple_model: + --multiple_model "$selExtraOpts.multiple_model" + #end if + ## (-r) + #if $selExtraOpts.constraint_file: + --constraint_file "$selExtraOpts.constraint_file" + #end if + ## (-R) + #if $selExtraOpts.bin_model_parameter_file: + --bin_model_parameter_file "$selExtraOpts.bin_model_parameter_file" + #end if + ## (-S) + #if $selExtraOpts.secondary_structure_file: + --secondary_structure_file "$selExtraOpts.secondary_structure_file" + #end if + ## (-t) + #if $selExtraOpts.start_tree_file: + --starting_tree "$selExtraOpts.start_tree_file" + #end if + ## (-T) see elsewhere + ## (-u) + $selExtraOpts.use_median_approximation + ## (-U) + $selExtraOpts.save_memory_gappy_alignments + ## (-V) + $selExtraOpts.disable_rate_heterogeneity + ## (-W) + #if $selExtraOpts.sliding_window_size: + --sliding_window_size $selExtraOpts.sliding_window_size + #end if + ## (-x) + #if str($selExtraOpts.rapid_bootstrap_random_seed): + --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed + #end if + ## (-y) + $selExtraOpts.parsimony_starting_tree_only + ## (-z) + #if $selExtraOpts.file_multiple_trees: + --file_multiple_trees "$selExtraOpts.file_multiple_trees" + #end if + + ## (-p) + #if $selExtraOpts.random_seed: + --random_seed $selExtraOpts.random_seed + #else + --random_seed 1234567890 + #end if + + #else: + --random_seed 1234567890 + #end if + </command> + <inputs> + <param type="data" format="fasta,phylip" name="infile" label="Source file" help="(-s)"/> + <conditional name="search_model_selector"> + <param name="model_type" type="select" label="Model Type" help="(--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" help="--base-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="aa_model_empirical_base_frequencies" + type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" /> + <param name="base_model" type="select" label="Substitution Model (--base_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" help="(--aa_search_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> + </when> + <when value="binary"> + <param name="base_model" type="select" label="Substitution Model" help="(--base_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> + <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"> + <param name="number_of_runs" type="integer" value="" + label="Number of runs" help="Specify the number of + alternative runs (-N|#) on distinct starting trees In combination + with the '-b' option will invoke a multiple boostrap analysis. + You can add the bootstopping criteria by choosing the autoMR, + autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of + providing a number here. Bootstopping will only work in + combination with '-x' or '-b'." + optional="True" /> + <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True" help="--number_of_runs_bootstop"> + <option value="" selected="yes"></option> + <option value="autoMR">autoMR</option> + <option value="autoMRE">autoMRE</option> + <option value="autoMRE_IGN">autoMRE_IGN</option> + <option value="autoFC">autoFC</option> + </param> + <param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" help="(-a)" /> + <param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True" + help="(--secondary_structure_model)"> + <option value="" selected="yes"></option> + <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" type="integer" value="" label="Random number for non-parametric bootstrapping" optional="True" help="(--bootseed)"/> + <param name="rapid_bootstrap_random_seed" type="integer" value='' label="Rapid bootstrapping random seed" optional="True" + help="Specify a random seed and turn 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. (-x)" /> + <param name="cutoff_threshold" type="float" label="MR Cutoff threshold" value="" + help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1. (-B)" optional="True"/> + <param name="numofcats" type="integer" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" help="(-c)" /> + <!-- (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now. --> + <param name="search_complete_random_tree" type="boolean" checked="False" truevalue="--search_complete_random_tree" falsevalue="" + display="checkboxes" label="Start ML optimization from a complete random starting tree" help="(--search_complete_random_tree)"/> + <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue="" + label="ML search convergence criterion" help="(--ml_search_convergence)" /> + <param name="model_opt_precision" type="float" label="Model optimization precision" value="" + help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used (--model_opt_precision)" optional="True" /> + <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" help="(-E)" /> + <param name="search_algorithm" type="select" label="Algorithm to execute" help="(-f)" 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">Hill-climbing ML Search (d) (default)</option> + <option value="e">Optimize GAMMA/GAMMAI model/branches (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" type="boolean" checked="no" truevalue="--save_memory_cat_model" falsevalue="" + display="checkboxes" label="ML tree searches under CAT model" optional="True" + 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 (--save_memory_cat_model)" /> + <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" help="(-g)" /> + <param name="enable_evol_heuristics" type="float" label="Enable the ML-based evolutionary placement algorithm heuristics" + help="Enable the ML-based evolutionary placement algorithm heuristics by specifiyng a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML). (--enable_evol_heuristics)" optional="True" > + <validator type="in_range" message="0.0 <= fraction <= 1.0" min="0.0" max="1.0"/> + </param> + <param name="initial_rearrangement_setting" type="integer" value="" label="Initial rearrangement setting" optional="True" help="(-i)"/> + <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True" help="(-I)"> + <option value="" selected="True"></option> + <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" type="select" label="Compute consensus tree" optional="True" help="(-J)"> + <option value="" selected="True"></option> + <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" type="boolean" checked="no" truevalue="--print_branch_lengths" falsevalue="" display="checkboxes" label="Print bootstrapped trees with branch lengths" help="Specifies that bootstrapped trees should be printed with branch lengths. 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. (-k)" optional="True" /> + <param name="multistate_sub_model" type="select" optional="True" label="Specify a multi-state substitution model" help="(-K)"> + <option value="" selected="true"></option> + <option value="GTR">GTR</option> + <option value="ORDERED">ORDERED</option> + <option value="MK">MK</option> + </param> + <param name="estimate_individual_branch_lengths" type="boolean" checked="no" + truevalue="--estimate_individual_branch_lengths" falsevalue="" display="checkboxes" + label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file (-M)." optional="True" /> + <param name="outgroup_name" type="text" value="" label="Outgroup name" + help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed. (-o)" optional="True" /> + <param name="disable_undetermined_seq_check" type="boolean" checked="no" + truevalue="--disable_undertermined_seq_check" falsevalue="" display="checkboxes" label="Disable check for completely undetermined sequence in alignment" optional="True" help="Disable the check for completely undetermined sequence in alignment. The program will not exit with an error message when '-O' is specified." /> + <param name="external_protein_model" format="txt" type="data" label="External AA substitution model" + help="Specify the file name of a user-defined AA (Protein) substitution model. 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. (--external_protein_model)" optional="True" /> + <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" optional="True" + help="Specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual. (--multiple_model)" /> + <param name="constraint_file" format="txt" type="data" label="Binary constraint tree" optional="True" + help="Specify the file name of a binary constraint tree. This tree does not need to be comprehensive, i.e. must not contain all taxa. (--constrain_file)" /> + <param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file" optional="True" + help="Specify the file name of a binary model parameter file that has previously been generated with RAxML using the '-f e' tree evaluation option. (-R)" /> + <param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file" optional="True" + help="Specify the name of a secondary structure file. The file can contain '.' for alignment columns that do not form part of a stem and characters '()<>[]{}' to define stem regions and pseudoknots. (-S)"/> + <param name="start_tree_file" format="txt" type="data" label="Starting tree file" optional="True" + help="Specify a user starting tree file name in Newick format. (-t)" /> + <param name="use_median_approximation" type="boolean" checked="no" truevalue="--use_median_approximation" falsevalue="" display="checkboxes" label="Use the median for the discrete approximation" + help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity. (-T)" optional="True" /> + <param name="save_memory_gappy_alignments" type="boolean" checked="no" truevalue="--save_memory_gappy_alignments" falsevalue="" display="checkboxes" label="Save memory on large gappy alignments" + help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments. (-U)" optional="True" /> + <param name="disable_rate_heterogeneity" type="boolean" checked="no" truevalue="--disable_raite_heterogeneity" falsevalue="" display="checkboxes" label="Disable rate heterogeneity" help="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead. Only works if you specify the CAT model of rate heterogeneity. (_V)" optional="True" /> + <param name="sliding_window_size" type="integer" value="" label="Sliding window size" optional="True" + help="Sliding window size for leave-one-out site-specific placement bias algorithm. Only effective when used in combination with '-f S'. Default is '100 sites' (-W)" /> + <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="--parsimony_starting_tree_only" falsevalue="" display="checkboxes" + label="Compute a randomized parsimony starting tree only" optional="True" + help="If you want to only compute a parsimony starting tree with RAxML specify '-y'. The program will exit after computation of the starting tree." /> + <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file" + help="Specify the file name of a file containing multiple trees e.g. from a bootstrap that shall be used to draw bipartition values onto a tree provided with '-t', It can also be used to compute per site log likelihoods in combination with '-f g' and to read a bunch of trees for '-f h', '-f m' and '-f n'. (-z)" optional="True" /> + <param name="random_seed" type="integer" value="1234567890" label="Random + seed used for the parsimony inferences" help="(--random_seed)"/> + </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>(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>(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>(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>(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" /> + <output name="bestTree"> + <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"> + <assert_contents> + <has_text_matching expression="Chicken" /> + <has_text_matching expression="RUN.4" /> + </assert_contents> + </output> + <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" lines_diff="30"/> + <output name="bestTree"> + <assert_contents> + <has_text_matching expression="Whale" /> + </assert_contents> + </output> + </test> + </tests> + <help> + +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/ + + +**Tool development**: + +Oleksandr Moskalenko with adaptations from Tiago Antao. + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu033</citation> + </citations> +</tool>