Mercurial > repos > iuc > raxml
changeset 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 |
| files | raxml.py raxml.xml tool_dependencies.xml |
| diffstat | 3 files changed, 313 insertions(+), 636 deletions(-) [+] |
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--- a/raxml.py Mon Nov 14 14:03:39 2016 -0500 +++ b/raxml.py Tue Jun 27 16:27:39 2017 -0400 @@ -6,14 +6,6 @@ import fnmatch import glob import optparse -import os -import subprocess -import sys - - -def stop_err(msg): - sys.stderr.write("%s\n" % msg) - sys.exit() def getint(name): @@ -24,347 +16,91 @@ def __main__(): - usage = "usage: %prog -T <threads> -s <input> -n <output> -m <model> [optional arguments]" - # Parse the primary wrapper's command line options - parser = optparse.OptionParser(usage=usage) - # raxml binary name, hardcoded in the xml file - parser.add_option("--binary", action="store", type="string", dest="binary", help="Command to run") - # (-a) - parser.add_option("--weightfile", action="store", type="string", dest="weightfile", help="Column weight file") - # (-A) - parser.add_option("--secondary_structure_model", action="store", type="string", dest="secondary_structure_model", help="Secondary structure model") + parser = optparse.OptionParser() # (-b) - parser.add_option("--bootseed", action="store", type="int", dest="bootseed", help="Bootstrap random number seed") - # (-c) - parser.add_option("--numofcats", action="store", type="int", dest="numofcats", help="Number of distinct rate categories") - # (-d) - parser.add_option("--search_complete_random_tree", action="store_true", dest="search_complete_random_tree", help="Search with a complete random starting tree") - # (-D) - parser.add_option("--ml_search_convergence", action="store_true", dest="ml_search_convergence", help="ML search onvergence criterion") - # (-e) - parser.add_option("--model_opt_precision", action="store", type="float", dest="model_opt_precision", help="Model Optimization Precision (-e)") - # (-E) - parser.add_option("--excludefile", action="store", type="string", dest="excludefile", help="Exclude File Name") - # (-f) - parser.add_option("--search_algorithm", action="store", type="string", dest="search_algorithm", help="Search Algorithm") - # (-F) - parser.add_option("--save_memory_cat_model", action="store_true", dest="save_memory_cat_model", help="Save memory under CAT and GTRGAMMA models") - # (-g) - parser.add_option("--groupingfile", action="store", type="string", dest="groupingfile", help="Grouping File Name") - # (-G) - parser.add_option("--enable_evol_heuristics", action="store_true", dest="enable_evol_heuristics", help="Enable evol algo heuristics") - # (-i) - parser.add_option("--initial_rearrangement_setting", action="store", type="int", dest="initial_rearrangement_setting", help="Initial Rearrangement Setting") - # (-I) - parser.add_option("--posterior_bootstopping_analysis", action="store", type="string", dest="posterior_bootstopping_analysis", help="Posterior bootstopping analysis") - # (-J) - parser.add_option("--majority_rule_consensus", action="store", type="string", dest="majority_rule_consensus", help="Majority rule consensus") - # (-k) - parser.add_option("--print_branch_lengths", action="store_true", dest="print_branch_lengths", help="Print branch lengths") - # (-K) - parser.add_option("--multistate_sub_model", action="store", type="string", dest="multistate_sub_model", help="Multistate substitution model") - # (-m) - parser.add_option("--model_type", action="store", type="string", dest="model_type", help="Model Type") - parser.add_option("--base_model", action="store", type="string", dest="base_model", help="Base Model") - parser.add_option("--aa_empirical_freq", action="store_true", dest="aa_empirical_freq", help="Use AA Empirical base frequences") - parser.add_option("--aa_search_matrix", action="store", type="string", dest="aa_search_matrix", help="AA Search Matrix") - # (-n) - parser.add_option("--name", action="store", type="string", dest="name", help="Run Name") + parser.add_option("--bootseed", action="store", type="int", dest="bootseed", help="Random number for non-parametric bootstrapping") # (-N/#) - parser.add_option("--number_of_runs", action="store", type="int", dest="number_of_runs", help="Number of alternative runs") - parser.add_option("--number_of_runs_bootstop", action="store", type="string", dest="number_of_runs_bootstop", help="Number of alternative runs based on the bootstop criteria") - # (-M) - parser.add_option("--estimate_individual_branch_lengths", action="store_true", dest="estimate_individual_branch_lengths", help="Estimate individual branch lengths") - # (-o) - parser.add_option("--outgroup_name", action="store", type="string", dest="outgroup_name", help="Outgroup Name") - # (-O) - parser.add_option("--disable_undetermined_seq_check", action="store_true", dest="disable_undetermined_seq_check", help="Disable undetermined sequence check") - # (-p) - parser.add_option("--random_seed", action="store", type="int", dest="random_seed", help="Random Number Seed") - # (-P) - parser.add_option("--external_protein_model", action="store", type="string", dest="external_protein_model", help="External Protein Model") + parser.add_option("--number_of_runs", action="store", type="int", dest="number_of_runs", default=1, help="Number of alternative runs") # (-q) parser.add_option("--multiple_model", action="store", type="string", dest="multiple_model", help="Multiple Model File") - # (-r) - parser.add_option("--constraint_file", action="store", type="string", dest="constraint_file", help="Constraint File") - # (-R) - parser.add_option("--bin_model_parameter_file", action="store", type="string", dest="bin_model_parameter_file", help="Constraint File") - # (-s) - parser.add_option("--source", action="store", type="string", dest="source", help="Input file") - # (-S) - parser.add_option("--secondary_structure_file", action="store", type="string", dest="secondary_structure_file", help="Secondary structure file") - # (-t) - parser.add_option("--starting_tree", action="store", type="string", dest="starting_tree", help="Starting Tree") - # (-T) - parser.add_option("--threads", action="store", type="int", dest="threads", help="Number of threads to use") - # (-u) - parser.add_option("--use_median_approximation", action="store_true", dest="use_median_approximation", help="Use median approximation") - # (-U) - parser.add_option("--save_memory_gappy_alignments", action="store_true", dest="save_memory_gappy_alignments", help="Save memory in large gapped alignments") - # (-V) - parser.add_option("--disable_rate_heterogeneity", action="store_true", dest="disable_rate_heterogeneity", help="Disable rate heterogeneity") - # (-W) - parser.add_option("--sliding_window_size", action="store", type="string", dest="sliding_window_size", help="Sliding window size") # (-x) parser.add_option("--rapid_bootstrap_random_seed", action="store", type="int", dest="rapid_bootstrap_random_seed", help="Rapid Boostrap Random Seed") - # (-y) - parser.add_option("--parsimony_starting_tree_only", action="store_true", dest="parsimony_starting_tree_only", help="Generate a parsimony starting tree only") - # (-z) - parser.add_option("--file_multiple_trees", action="store", type="string", dest="file_multiple_trees", help="Multiple Trees File") (options, args) = parser.parse_args() - cmd = [] - - # Required parameters - binary = options.binary - cmd.append(binary) - # Threads - if options.threads > 1: - threads = "-T %d" % options.threads - cmd.append(threads) - # Source - source = "-s %s" % options.source - cmd.append(source) - # Hardcode to "galaxy" first to simplify the output part of the wrapper - # name = "-n %s" % options.name - name = "-n galaxy" - cmd.append(name) - # Model - model_type = options.model_type - base_model = options.base_model - aa_search_matrix = options.aa_search_matrix - aa_empirical_freq = options.aa_empirical_freq - if model_type == 'aminoacid': - model = "-m %s%s" % (base_model, aa_search_matrix) - if aa_empirical_freq: - model = "-m %s%s%s" % (base_model, aa_search_matrix, 'F') - # (-P) - if options.external_protein_model: - external_protein_model = "-P %s" % options.external_protein_model - cmd.append(external_protein_model) - else: - model = "-m %s" % base_model - cmd.append(model) - if model == "GTRCAT": - # (-c) - if options.numofcats: - numofcats = "-c %d" % options.numofcats - cmd.append(numofcats) - # Optional parameters - if options.number_of_runs_bootstop: - number_of_runs_bootstop = "-N %s" % options.number_of_runs_bootstop - cmd.append(number_of_runs_bootstop) - else: - number_of_runs_bootstop = '' - if options.number_of_runs: - number_of_runs_opt = "-N %d" % options.number_of_runs - cmd.append(number_of_runs_opt) - else: - number_of_runs_opt = 0 - # (-a) - if options.weightfile: - weightfile = "-a %s" % options.weightfile - cmd.append(weightfile) - # (-A) - if options.secondary_structure_model: - secondary_structure_model = "-A %s" % options.secondary_structure_model - cmd.append(secondary_structure_model ) - # (-b) - if options.bootseed: - bootseed = "-b %d" % options.bootseed - cmd.append(bootseed) - else: - bootseed = 0 - # -C - doesn't work in pthreads version, skipped - if options.search_complete_random_tree: - cmd.append("-d") - if options.ml_search_convergence: - cmd.append("-D" ) - if options.model_opt_precision: - model_opt_precision = "-e %f" % options.model_opt_precision - cmd.append(model_opt_precision) - if options.excludefile: - excludefile = "-E %s" % options.excludefile - cmd.append(excludefile) - if options.search_algorithm: - search_algorithm = "-f %s" % options.search_algorithm - cmd.append(search_algorithm) - if options.save_memory_cat_model: - cmd.append("-F") - if options.groupingfile: - groupingfile = "-g %s" % options.groupingfile - cmd.append(groupingfile) - if options.enable_evol_heuristics: - enable_evol_heuristics = "-G %f" % options.enable_evol_heuristics - cmd.append(enable_evol_heuristics ) - if options.initial_rearrangement_setting: - initial_rearrangement_setting = "-i %s" % options.initial_rearrangement_setting - cmd.append(initial_rearrangement_setting) - if options.posterior_bootstopping_analysis: - posterior_bootstopping_analysis = "-I %s" % options.posterior_bootstopping_analysis - cmd.append(posterior_bootstopping_analysis) - if options.majority_rule_consensus: - majority_rule_consensus = "-J %s" % options.majority_rule_consensus - cmd.append(majority_rule_consensus) - if options.print_branch_lengths: - cmd.append("-k") - if options.multistate_sub_model: - multistate_sub_model = "-K %s" % options.multistate_sub_model - cmd.append(multistate_sub_model) - if options.estimate_individual_branch_lengths: - cmd.append("-M") - if options.outgroup_name: - outgroup_name = "-o %s" % options.outgroup_name - cmd.append(outgroup_name) - if options.disable_undetermined_seq_check: - cmd.append("-O") - if options.random_seed: - random_seed = "-p %d" % options.random_seed - cmd.append(random_seed) - multiple_model = None - if options.multiple_model: - multiple_model = "-q %s" % options.multiple_model - cmd.append(multiple_model) - if options.constraint_file: - constraint_file = "-r %s" % options.constraint_file - cmd.append(constraint_file) - if options.bin_model_parameter_file: - bin_model_parameter_file_name = "RAxML_binaryModelParameters.galaxy" - os.symlink(options.bin_model_parameter_file, bin_model_parameter_file_name ) - bin_model_parameter_file = "-R %s" % options.bin_model_parameter_file - # Needs testing. Is the hardcoded name or the real path needed? - cmd.append(bin_model_parameter_file) - if options.secondary_structure_file: - secondary_structure_file = "-S %s" % options.secondary_structure_file - cmd.append(secondary_structure_file) - if options.starting_tree: - starting_tree = "-t %s" % options.starting_tree - cmd.append(starting_tree) - if options.use_median_approximation: - cmd.append("-u") - if options.save_memory_gappy_alignments: - cmd.append("-U") - if options.disable_rate_heterogeneity: - cmd.append("-V") - if options.sliding_window_size: - sliding_window_size = "-W %d" % options.sliding_window_size - cmd.append(sliding_window_size) - if options.rapid_bootstrap_random_seed: - rapid_bootstrap_random_seed = "-x %d" % options.rapid_bootstrap_random_seed - cmd.append(rapid_bootstrap_random_seed) - else: - rapid_bootstrap_random_seed = 0 - if options.parsimony_starting_tree_only: - cmd.append("-y") - if options.file_multiple_trees: - file_multiple_trees = "-z %s" % options.file_multiple_trees - cmd.append(file_multiple_trees) - - print "cmd list: ", cmd, "\n" - - full_cmd = " ".join(cmd) - print "Command string: %s" % full_cmd - - try: - proc = subprocess.Popen(args=full_cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) - except Exception as err: - sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err)) - sys.exit(1) - stdout, stderr = proc.communicate() - return_code = proc.returncode - if return_code: - sys.stdout.write(stdout) - sys.stderr.write(stderr) - sys.stderr.write("Return error code %i from command:\n" % return_code) - sys.stderr.write("%s\n" % cmd) - else: - sys.stdout.write(stdout) - sys.stdout.write(stderr) # Multiple runs - concatenate - if number_of_runs_opt > 0: - if (bootseed == 0) and (rapid_bootstrap_random_seed == 0 ): + if options.number_of_runs > 1: + if options.bootseed is None and options.rapid_bootstrap_random_seed is None: runfiles = glob.glob('RAxML*RUN*') runfiles.sort(key=getint) - # Logs - outfile = open('RAxML_log.galaxy', 'w') - for filename in runfiles: - if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'): - infile = open(filename, 'r') - filename_line = "%s\n" % filename - outfile.write(filename_line) - for line in infile: - outfile.write(line) - infile.close() - outfile.close() - # Parsimony Trees - outfile = open('RAxML_parsimonyTree.galaxy', 'w') - for filename in runfiles: - if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'): - infile = open(filename, 'r') - filename_line = "%s\n" % filename - outfile.write(filename_line) - for line in infile: - outfile.write(line) - infile.close() - outfile.close() - # Results - outfile = open('RAxML_result.galaxy', 'w') - for filename in runfiles: - if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'): - infile = open(filename, 'r') - filename_line = "%s\n" % filename - outfile.write(filename_line) - for line in infile: - outfile.write(line) - infile.close() - outfile.close() + # Logs + with open('RAxML_log.galaxy', 'w') as outfile: + for filename in runfiles: + if fnmatch.fnmatch(filename, 'RAxML_log.galaxy.RUN.*'): + with open(filename, 'r') as infile: + filename_line = "%s\n" % filename + outfile.write(filename_line) + for line in infile: + outfile.write(line) + # Parsimony Trees + with open('RAxML_parsimonyTree.galaxy', 'w') as outfile: + for filename in runfiles: + if fnmatch.fnmatch(filename, 'RAxML_parsimonyTree.galaxy.RUN.*'): + with open(filename, 'r') as infile: + filename_line = "%s\n" % filename + outfile.write(filename_line) + for line in infile: + outfile.write(line) + # Results + with open('RAxML_result.galaxy', 'w') as outfile: + for filename in runfiles: + if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.RUN.*'): + with open(filename, 'r') as infile: + filename_line = "%s\n" % filename + outfile.write(filename_line) + for line in infile: + outfile.write(line) # Multiple Model Partition Files - if multiple_model: + if options.multiple_model: files = glob.glob('RAxML_bestTree.galaxy.PARTITION.*') if len(files) > 0: files.sort(key=getint) - outfile = open('RAxML_bestTreePartitions.galaxy', 'w') # Best Tree Partitions - for filename in files: - if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'): - infile = open(filename, 'r') - filename_line = "%s\n" % filename - outfile.write(filename_line) - for line in infile: - outfile.write(line) - infile.close() - outfile.close() + with open('RAxML_bestTreePartitions.galaxy', 'w') as outfile: + for filename in files: + if fnmatch.fnmatch(filename, 'RAxML_bestTree.galaxy.PARTITION.*'): + with open(filename, 'r') as infile: + filename_line = "%s\n" % filename + outfile.write(filename_line) + for line in infile: + outfile.write(line) else: - outfile = open('RAxML_bestTreePartitions.galaxy', 'w') - outfile.write("No partition files were produced.\n") - outfile.close() + with open('RAxML_bestTreePartitions.galaxy', 'w') as outfile: + outfile.write("No partition files were produced.\n") # Result Partitions files = glob.glob('RAxML_result.galaxy.PARTITION.*') if len(files) > 0: files.sort(key=getint) - outfile = open('RAxML_resultPartitions.galaxy', 'w') - for filename in files: - if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'): - infile = open(filename, 'r') - filename_line = "%s\n" % filename - outfile.write(filename_line) - for line in infile: - outfile.write(line) - infile.close() - outfile.close() + with open('RAxML_resultPartitions.galaxy', 'w') as outfile: + for filename in files: + if fnmatch.fnmatch(filename, 'RAxML_result.galaxy.PARTITION.*'): + with open(filename, 'r') as infile: + filename_line = "%s\n" % filename + outfile.write(filename_line) + for line in infile: + outfile.write(line) else: - outfile = open('RAxML_resultPartitions.galaxy', 'w') - outfile.write("No partition files were produced.\n") - outfile.close() + with open('RAxML_resultPartitions.galaxy', 'w') as outfile: + outfile.write("No partition files were produced.\n") # DEBUG options - infof = open('RAxML_info.galaxy', 'a') - infof.write('\nOM: CLI options DEBUG START:\n') - infof.write(options.__repr__()) - infof.write('\nOM: CLI options DEBUG END\n') + with open('RAxML_info.galaxy', 'a') as infof: + infof.write('\nOM: CLI options DEBUG START:\n') + infof.write(options.__repr__()) + infof.write('\nOM: CLI options DEBUG END\n') + if __name__ == "__main__": __main__()
--- 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>
--- a/tool_dependencies.xml Mon Nov 14 14:03:39 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="raxml" version="8.2.4"> - <repository changeset_revision="34be595fd2a9" name="package_raxml_8_2_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>