raxml: raxml.xml comparison

comparison 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

comparison

equal deleted inserted replaced

-:6805e85573b8
+:ba29b5e2a4be
-<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
+<command detect_errors="exit_code"><![CDATA[
-## Required parameters
+## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
-## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
+#set $slots = $getVar('GALAXY_SLOTS', 1)
-## (-T)
+#if $slots == 1:
-## Cannot have --threads 1
+raxmlHPC
-#set $slots = $getVar('GALAXY_SLOTS', 1)
+## Cannot have -T 1
-#if $slots == 1:
+#else:
---binary "raxmlHPC"
+raxmlHPC-PTHREADS
---threads 1
+-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 $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:
---binary "raxmlHPC-PTHREADS"
+-N $selExtraOpts.number_of_runs_conditional.number_of_runs_bootstop
---threads $slots
+#end if
-#end if
+#if $selExtraOpts.weightfile:
-## (-s)
+-a '$selExtraOpts.weightfile'
---source "$infile"
+#end if
-## (-m)
+#if $selExtraOpts.secondary_structure_model:
---model_type $search_model_selector.model_type
+-A $selExtraOpts.secondary_structure_model
---base_model $search_model_selector.base_model
+#end if
-#if str( $search_model_selector.model_type ) == 'aminoacid':
+#if str($selExtraOpts.bootseed):
-$search_model_selector.aa_model_empirical_base_frequencies
+-b $selExtraOpts.bootseed
-#if $search_model_selector.aa_search_matrix:
+#end if
---aa_search_matrix $search_model_selector.aa_search_matrix
+-B $selExtraOpts.cutoff_threshold
-#end if
+-c $selExtraOpts.numofcats
-#end if
+$selExtraOpts.search_complete_random_tree
+$selExtraOpts.ml_search_convergence
-## Optional parameters
+#if $selExtraOpts.model_opt_precision:
+-e $selExtraOpts.model_opt_precision
-#if str( $selExtraOpts.extraOptions ) == 'full':
+#end if
-## (-N/#)
+#if $selExtraOpts.excludefile:
-#if $selExtraOpts.number_of_runs:
+-E '$selExtraOpts.excludefile'
---number_of_runs $selExtraOpts.number_of_runs
+#end if
-#end if
+#if $selExtraOpts.search_algorithm:
-#if $selExtraOpts.number_of_runs_bootstop:
+-f $selExtraOpts.search_algorithm
---number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop
+#end if
-#end if
+$selExtraOpts.save_memory_cat_model
-## (-a)
+#if $selExtraOpts.groupingfile:
-#if $selExtraOpts.weightfile:
+-g '$selExtraOpts.groupingfile'
---weightfile "$selExtraOpts.weightfile"
+#end if
-#end if
+#if $selExtraOpts.enable_evol_heuristics:
-## (-b)
+-G $selExtraOpts.enable_evol_heuristics
-#if str ($selExtraOpts.secondary_structure_model) != "":
+#end if
---secondary_structure_model $selExtraOpts.secondary_structure_model
+#if str($selExtraOpts.initial_rearrangement_setting):
-#end if
+-i $selExtraOpts.initial_rearrangement_setting
-## (-b)
+#end if
-#if str($selExtraOpts.bootseed):
+#if $selExtraOpts.posterior_bootstopping_analysis:
---bootseed $selExtraOpts.bootseed
+-I $selExtraOpts.posterior_bootstopping_analysis
 #end if
-## (-c)
+#if $selExtraOpts.majority_rule_consensus:
-#if $selExtraOpts.numofcats:
+-J $selExtraOpts.majority_rule_consensus
---numofcats $selExtraOpts.numofcats
+#end if
-#end if
+$selExtraOpts.print_branch_lengths
-## (-d)
+-K $selExtraOpts.multistate_sub_model
-$selExtraOpts.search_complete_random_tree
+$selExtraOpts.estimate_individual_branch_lengths
-## (-D)
+#if $selExtraOpts.outgroup_name:
-$selExtraOpts.ml_search_convergence
+-o '$selExtraOpts.outgroup_name'
-## (-e)
+#end if
-#if $selExtraOpts.model_opt_precision:
+$selExtraOpts.disable_undetermined_seq_check
---model_opt_precision $selExtraOpts.model_opt_precision
+#if $selExtraOpts.external_protein_model:
-#end if
+-P '$selExtraOpts.external_protein_model'
-## (-E)
+#end if
-#if $selExtraOpts.excludefile:
+#if $selExtraOpts.multiple_model:
---excludefile "$selExtraOpts.excludefile"
+-q '$selExtraOpts.multiple_model'
 #end if
-## (-f)
+#if $selExtraOpts.constraint_file:
-#if $selExtraOpts.search_algorithm:
+-r '$selExtraOpts.constraint_file'
---search_algorithm $selExtraOpts.search_algorithm
+#end if
-#end if
+#if $selExtraOpts.bin_model_parameter_file:
-## (-F)
+-R '$selExtraOpts.bin_model_parameter_file'
-$selExtraOpts.save_memory_cat_model
+#end if
-## (-g)
+#if $selExtraOpts.secondary_structure_file:
-#if $selExtraOpts.groupingfile:
+-S '$selExtraOpts.secondary_structure_file'
---groupingfile "$selExtraOpts.groupingfile"
+#end if
-#end if
+#if $selExtraOpts.start_tree_file:
-## (-G)
+-t '$selExtraOpts.start_tree_file'
-#if $selExtraOpts.enable_evol_heuristics:
+#end if
---enable_evol_heuristics $selExtraOpts.enable_evol_heuristics
+$selExtraOpts.use_median_approximation
-#end if
+$selExtraOpts.save_memory_gappy_alignments
-## (-i)
+$selExtraOpts.disable_rate_heterogeneity
-#if $selExtraOpts.initial_rearrangement_setting:
+-W $selExtraOpts.sliding_window_size
---initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting
+#if str($selExtraOpts.rapid_bootstrap_random_seed):
-#end if
+-x $selExtraOpts.rapid_bootstrap_random_seed
-## (-I)
+#end if
-#if $selExtraOpts.posterior_bootstopping_analysis:
+$selExtraOpts.parsimony_starting_tree_only
---posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis
+#end if
-#end if
+&& python '$__tool_directory__/raxml.py'
-## (-J)
+#if $selExtraOpts.extraOptions == 'full':
-#if $selExtraOpts.majority_rule_consensus:
+#if str($selExtraOpts.bootseed):
---majority_rule_consensus $selExtraOpts.majority_rule_consensus
+--bootseed $selExtraOpts.bootseed
 #end if
-## (-k)
+#if str($selExtraOpts.rapid_bootstrap_random_seed):
-$selExtraOpts.print_branch_lengths
+--rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed
-## (-K)
+#end if
-#if str ($selExtraOpts.multistate_sub_model) != "":
+#if $selExtraOpts.number_of_runs_conditional.number_of_runs_selector == 'by_number_of_runs':
---multistate_sub_model $selExtraOpts.multistate_sub_model
+--number_of_runs $selExtraOpts.number_of_runs_conditional.number_of_runs
 #end if
-## (-m) - see elsewhere
+#if $selExtraOpts.multiple_model:
-## (-M)
+--multiple_model '$selExtraOpts.multiple_model'
-$selExtraOpts.estimate_individual_branch_lengths
+#end if
-## (-n) - see elsewhere
+#end if
-## (-o)
+]]></command>
-#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)"/>
+<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">
+<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"
+<param name="base_model" type="select" label="Substitution model">
-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)">
+<param name="aa_search_matrix" type="select" label="Matrix">
 <option value="DAYHOFF" selected="true">DAYHOFF</option>
 <option value="DCMUT">DCMUT</option>
 <option value="JTT">JTT</option>
 <option value="MTREV">MTREV</option>
 <option value="WAG">WAG</option>
 <option value="DUMMY">DUMMY</option>
 <option value="DUMMY2">DUMMY2</option>
 <option value="GTR_UNLINKED">GTR_UNLINKED</option>
 <option value="GTR">GTR</option>
 </param>
+<param name="aa_model_empirical_base_frequencies" type="boolean" truevalue="F" falsevalue="" checked="no" display="checkboxes" label="Use empirical base frequencies in AA models" />
 </when>
 <when value="binary">
-<param name="base_model" type="select" label="Substitution Model" help="(--base_model)">
+<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">
+<param name="base_model" type="select" label="Substitution model">
 <option value="MULTICAT">MULTICAT</option>
 <option value="MULTICATI">MULTICATI</option>
 <option value="MULTIGAMMA">MULTIGAMMA</option>
 <option value="MULTIGAMMAI">MULTIGAMMAI</option>
 </param>
 </when>
 </conditional>
+<param name="random_seed" argument="-p" type="integer" value="1234567890" label="Random seed used for the parsimony inferences" />
 <conditional name="selExtraOpts">
 <param name="extraOptions" type="select" label="RAxML options to use"
 help="The required minimal settings are the input file and the
 substitution model. To specify extra options select the 'Full option list'">
 <option value="required">Required options only</option>
 <option value="full">Full option list</option>
 </param>
 <when value="required" />
 <when value="full">
-<param name="number_of_runs" type="integer" value=""
+<conditional name="number_of_runs_conditional">
-label="Number of runs" help="Specify the number of
+<param name="number_of_runs_selector" type="select" label="Multiple boostrap specification">
-alternative runs (-N|#) on distinct starting trees In combination
+<option value="by_number_of_runs">By number of runs</option>
-with the '-b' option will invoke a multiple boostrap analysis.
+<option value="by_bootstopping">By bootstopping criteria</option>
-You can add the bootstopping criteria by choosing the autoMR,
+</param>
-autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
+<when value="by_number_of_runs">
-providing a number here. Bootstopping will only work in
+<param name="number_of_runs" argument="-N" type="integer" value="1" label="Number of alternative runs on distinct starting trees"
-combination with '-x' or '-b'."
+help="In combination with the '-b' option, this will invoke a multiple boostrap analysis" />
-optional="True" />
+</when>
-<param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True" help="--number_of_runs_bootstop">
+<when value="by_bootstopping">
-<option value="" selected="yes"></option>
+<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>
-<param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" help="(-a)" />
+</when>
-<param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True"
+</conditional>
-help="(--secondary_structure_model)">
+<param name="weightfile" argument="-a" type="data" format="txt" optional="true" label="Column weight file" />
-<option value="" selected="yes"></option>
+<param name="secondary_structure_model" argument="-A" type="select" optional="true" label="Secondary structure substitution model">
 <option value="S6A">S6A</option>
 <option value="S6B">S6B</option>
 <option value="S6C">S6C</option>
 <option value="S6D">S6D</option>
 <option value="S6E">S6E</option>
 <option value="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="bootseed" argument="-b" type="integer" value="" optional="true" label="Random seed for non-parametric bootstrapping"
-<param name="rapid_bootstrap_random_seed" type="integer" value='' label="Rapid bootstrapping random seed" optional="True"
+help="Specifying a value turns on bootstrapping" />
-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="rapid_bootstrap_random_seed" argument="-x" type="integer" value="" optional="true" label="Random seed for rapid bootstrapping"
-<param name="cutoff_threshold" type="float" label="MR Cutoff threshold" value=""
+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" />
-help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1. (-B)" optional="True"/>
+<param name="cutoff_threshold" argument="-B" type="float" value="0.03" min="0" max="1" label="MR cutoff threshold"
-<param name="numofcats" type="integer" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" help="(-c)" />
+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=""
+<param name="search_complete_random_tree" argument="-d" type="boolean" truevalue="-d" falsevalue=""
-display="checkboxes" label="Start ML optimization from a complete random starting tree" help="(--search_complete_random_tree)"/>
+label="Start ML optimization from a complete random starting tree" />
-<param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue=""
+<param name="ml_search_convergence" argument="-D" type="boolean" truevalue="-D" falsevalue=""
-label="ML search convergence criterion" help="(--ml_search_convergence)" />
+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" type="float" label="Model optimization precision" value=""
+<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 when MIX/MIXI or GAMMA/GAMMAI models are used (--model_opt_precision)" optional="True" />
+help="Set model optimization precision in log likelihood units for final optimization of tree topology" />
-<param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" help="(-E)" />
+<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" type="select" label="Algorithm to execute" help="(-f)" optional="True">
+<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="d" selected="true">New rapid hill-climbing (d)</option>
-<option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option>
+<option value="D">Rapid hill-climbing with RELL bootstraps (D)</option>
+<option value="e">Optimize model+branch lengths under GAMMA/GAMMAI only (e)</option>
 <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
 <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
 <option value="j">Generate bootstrapped alignment files (j)</option>
 <option value="J">Compute SH-like support values for the -t tree (J)</option>
 <option value="m">Compare bipartitions between -t and -z trees (m)</option>
 <option value="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=""
+<param name="save_memory_cat_model" argument="-F" type="boolean" truevalue="-F" falsevalue=""
-display="checkboxes" label="ML tree searches under CAT model" optional="True"
+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 (--save_memory_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" format="txt" type="data" label="Multifurcating constraint tree" optional="True" help="(-g)" />
+<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" type="float" label="Enable the ML-based evolutionary placement algorithm heuristics"
+<param name="enable_evol_heuristics" argument="-G" type="float" min="0.0" max="1.0" optional="true"
-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" >
+label="Enable the ML-based evolutionary placement algorithm heuristics"
-<validator type="in_range" message="0.0 &lt;= fraction &lt;= 1.0" min="0.0" max="1.0"/>
+help="By specifying a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML)" />
-</param>
+<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="initial_rearrangement_setting" type="integer" value="" label="Initial rearrangement setting" optional="True" help="(-i)"/>
+<param name="posterior_bootstopping_analysis" argument="-I" type="select" optional="true" label="A posteriori bootstopping analysis">
-<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)">
+<param name="majority_rule_consensus" argument="-J" type="select" optional="true" label="Compute consensus tree">
-<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="print_branch_lengths" argument="-k" type="boolean" truevalue="-k" falsevalue=""
-<param name="multistate_sub_model" type="select" optional="True" label="Specify a multi-state substitution model" help="(-K)">
+label="Print bootstrapped trees with branch lengths"
-<option value="" selected="true"></option>
+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" />
-<option value="GTR">GTR</option>
+<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"
+<param name="estimate_individual_branch_lengths" argument="-M" type="boolean" truevalue="-M" falsevalue=""
-truevalue="--estimate_individual_branch_lengths" falsevalue="" display="checkboxes"
+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" />
-label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file (-M)." optional="True" />
+<param name="outgroup_name" argument="-o" type="text" value="" optional="true" label="Outgroup name"
-<param name="outgroup_name" type="text" value="" label="Outgroup name"
+help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed" />
-help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed. (-o)" optional="True" />
+<param name="disable_undetermined_seq_check" argument="-O" type="boolean" truevalue="-O" falsevalue=""
-<param name="disable_undetermined_seq_check" type="boolean" checked="no"
+label="Disable check for completely undetermined sequence in alignment"
-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." />
+help="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"
+<param name="external_protein_model" argument="-P" type="data" format="txt" optional="true" label="External AA (Protein) 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" />
+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" format="txt" type="data" label="Multiple model assignment to alignment partitions" optional="True"
+<param name="multiple_model" argument="-q" type="data" format="txt" 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)" />
+label="Assignment of models to alignment partitions for multiple models of substitution"
-<param name="constraint_file" format="txt" type="data" label="Binary constraint tree" optional="True"
+help="For the syntax of this file please consult the RaXML manual" />
-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="constraint_file" argument="-r" type="data" format="txt" optional="true" label="Binary constraint tree"
-<param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file" optional="True"
+help="This tree does not need to be comprehensive, i.e. does not have to contain all taxa" />
-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="bin_model_parameter_file" argument="-R" type="data" format="txt" optional="true" label="Binary model parameter file"
-<param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file" optional="True"
+help="This parameter file can be generated with RAxML using the '-f e' tree evaluation option" />
-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="secondary_structure_file" argument="-S" type="data" format="txt" optional="true" label="Secondary structure file"
-<param name="start_tree_file" format="txt" type="data" label="Starting tree file" optional="True"
+help="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" />
-help="Specify a user starting tree file name in Newick format. (-t)" />
+<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" type="boolean" checked="no" truevalue="--use_median_approximation" falsevalue="" display="checkboxes" label="Use the median for the discrete approximation"
+<param name="use_median_approximation" argument="-u" type="boolean" truevalue="-u" falsevalue=""
-help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity. (-T)" optional="True" />
+label="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity" />
-<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"
+<param name="save_memory_gappy_alignments" argument="-U" type="boolean" truevalue="-U" falsevalue=""
-help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments. (-U)" optional="True" />
+label="Save memory on large gappy alignments"
-<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" />
+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="sliding_window_size" type="integer" value="" label="Sliding window size" optional="True"
+<param name="disable_rate_heterogeneity" argument="-V" type="boolean" truevalue="-V" falsevalue=""
-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)" />
+label="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead"
-<param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="--parsimony_starting_tree_only" falsevalue="" display="checkboxes"
+help="Only works if you specify the CAT model of rate heterogeneity" />
-label="Compute a randomized parsimony starting tree only" optional="True"
+<param name="sliding_window_size" argument="-W" type="integer" min="1" value="100"
-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." />
+label="Sliding window size for leave-one-out site-specific placement bias algorithm"
-<param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file"
+help="Only effective when used in combination with '-f S'" />
-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="parsimony_starting_tree_only" argument="-y" type="boolean" truevalue="-y" falsevalue=""
-<param name="random_seed" type="integer" value="1234567890" label="Random
+label="Compute a randomized parsimony starting tree only"
-seed used for the parsimony inferences" help="(--random_seed)"/>
+help="The program will exit after computation of the starting tree" />
 </when>
 </conditional>
 </inputs>
 <outputs>
 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />
 <!-- REQUIRED -->
 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">
-<filter>(selExtraOpts['extraOptions'] == 'required')</filter>
+<filter>selExtraOpts['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 -->
 <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['extraOptions'] == 'full'</filter> -->
-<!-- <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
+<!-- <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
-<filter>(selExtraOpts['majority_rule_consensus'] == '')</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['extraOptions'] == "full"</filter>
-<filter>(selExtraOpts['multiple_model'] != '')</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['extraOptions'] == "full"</filter>
-<filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
+<filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter>
-<filter>(selExtraOpts['bootseed'] == '')</filter>
+<filter>selExtraOpts['bootseed'] == ''</filter>
-<filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
+<filter>selExtraOpts['search_algorithm'] != 'a'</filter>
-<filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
+<filter>selExtraOpts['search_algorithm'] != 'b'</filter>
-<filter>(selExtraOpts['majority_rule_consensus'] == '') </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['extraOptions'] == "full"</filter>
-<filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</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['extraOptions'] == "full"</filter>
-<filter>(selExtraOpts['multiple_model'] is not None)</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['rapid_bootstrap_random_seed'] == ''</filter>
-<filter>(selExtraOpts['bootseed'] == '')</filter>
+<filter>selExtraOpts['bootseed'] == ''</filter>
-<filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
+<filter>selExtraOpts['search_algorithm'] != 'a'</filter>
-<filter>(selExtraOpts['constraint_file'] is None)</filter>
+<filter>selExtraOpts['constraint_file'] is None</filter>
-<filter>(selExtraOpts['groupingfile'] is None)</filter>
+<filter>selExtraOpts['groupingfile'] is None</filter>
-<filter>(selExtraOpts['search_complete_random_tree'] is False)</filter>
+<filter>selExtraOpts['search_complete_random_tree'] is False</filter>
-<filter>(selExtraOpts['start_tree_file'] is None)</filter>
+<filter>selExtraOpts['start_tree_file'] is None</filter>
-<filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
+<filter>not selExtraOpts['majority_rule_consensus'] == ''</filter>
 -->
 </data>
 <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
 <filter>selExtraOpts['extraOptions'] == "full"</filter>
 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
 </data>
 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions">
-<filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
+<filter>selExtraOpts['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>
 <filter>selExtraOpts['extraOptions'] == "full"</filter>
 </data>
 <has_text_matching expression="Whale" />
 </assert_contents>
 </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/web/software/raxml/
-.. _RAxML: http://www.exelixis-lab.org/
 **Tool development**:
 Oleksandr Moskalenko with adaptations from Tiago Antao.
+]]></help>
-</help>
 <citations>
 <citation type="doi">10.1093/bioinformatics/btu033</citation>
 </citations>
 </tool>

Mercurial > repos > iuc > raxml

comparison raxml.xml @ 1:ba29b5e2a4be draft