annotate raxml.xml @ 0:6805e85573b8 draft

planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f

<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 &lt;= fraction &lt;= 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 '()&lt;&gt;[]{}' 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>