Mercurial > repos > iuc > raxml
diff raxml.xml @ 1:ba29b5e2a4be draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
| author | iuc |
|---|---|
| date | Tue, 27 Jun 2017 16:27:39 -0400 |
| parents | 6805e85573b8 |
| children | a4b71be30c3c |
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--- a/raxml.xml Mon Nov 14 14:03:39 2016 -0500 +++ b/raxml.xml Tue Jun 27 16:27:39 2017 -0400 @@ -1,197 +1,146 @@ -<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.2"> +<tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4"> <description>- Maximum Likelihood based inference of large phylogenetic trees</description> <requirements> - <requirement type='package' version="8.2.4">raxml</requirement> + <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 + <command detect_errors="exit_code"><![CDATA[ +## binary is hard-coded to the pthreads enabled raxml executable if threads > 1 +#set $slots = $getVar('GALAXY_SLOTS', 1) +#if $slots == 1: + raxmlHPC + ## Cannot have -T 1 +#else: + raxmlHPC-PTHREADS + -T $slots +#end if +-s '$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 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 - +#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: - --random_seed 1234567890 + -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 - </command> + $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 type="data" format="fasta,phylip" name="infile" label="Source file" help="(-s)"/> + <param name="infile" argument="-s" type="data" format="fasta,phylip" label="Source file" /> <conditional name="search_model_selector"> - <param name="model_type" type="select" label="Model Type" help="(--model_type)"> + <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" help="--base-model"> - <option value="GTRCAT">GTRCAT</option> - <option value="GTRCATI">GTRCATI</option> + <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="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)"> + <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" help="(--aa_search_matrix)"> + <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> @@ -215,24 +164,26 @@ <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" help="(--base_model)"> - <option value="BINCAT">BINCAT</option> - <option value="BINCATI">BINCATI</option> - <option value="BINGAMMA">BINGAMMA</option> - <option value="BINGAMMAI">BINGAMMAI</option> + <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 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 @@ -242,26 +193,26 @@ </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> + <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> @@ -277,27 +228,29 @@ <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)" /> + <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" 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"> + <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">Hill-climbing ML Search (d) (default)</option> - <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</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> @@ -318,71 +271,69 @@ <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> + <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" type="select" label="Compute consensus tree" optional="True" help="(-J)"> - <option value="" selected="True"></option> + <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" 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> + <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" 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)"/> + <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> @@ -390,15 +341,15 @@ <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['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['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['extraOptions'] == 'required'</filter> <filter>selExtraOpts['search_algorithm'] != 'a'</filter> </data> <!-- ADVANCED --> @@ -407,49 +358,49 @@ <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> --> + <!-- <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> + <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['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> + <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['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> + <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> + <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['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> + <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"> @@ -458,24 +409,24 @@ <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['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> + <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> + <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> + <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> + <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> @@ -523,22 +474,18 @@ </output> </test> </tests> - <help> - + <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/ - +.. _RAxML: http://www.exelixis-lab.org/web/software/raxml/ **Tool development**: Oleksandr Moskalenko with adaptations from Tiago Antao. - - </help> + ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btu033</citation> </citations>