# HG changeset patch
# User iuc
# Date 1498595259 14400
# Node ID ba29b5e2a4be345857a03bd97bcded286b1ad7ed
# Parent  6805e85573b8976b6980c9891b0c6be6193a283f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069

diff -r 6805e85573b8 -r ba29b5e2a4be raxml.py
--- 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__()
diff -r 6805e85573b8 -r ba29b5e2a4be raxml.xml
--- 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 &lt;= fraction &lt;= 1.0" min="0.0" max="1.0"/>
-                </param>
-                <param name="initial_rearrangement_setting" type="integer" value="" label="Initial rearrangement setting" optional="True" help="(-i)"/>
-                <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True" help="(-I)">
-                    <option value="" selected="True"></option>
+                <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 '()&lt;&gt;[]{}' to define stem regions and pseudoknots. (-S)"/>
-                <param name="start_tree_file" format="txt" type="data" label="Starting tree file" optional="True"
-                    help="Specify a user starting tree file name in Newick format. (-t)" />
-                <param name="use_median_approximation" type="boolean" checked="no" truevalue="--use_median_approximation" falsevalue="" display="checkboxes" label="Use the median for the discrete approximation"
-                    help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity. (-T)" optional="True" />
-                <param name="save_memory_gappy_alignments" type="boolean" checked="no" truevalue="--save_memory_gappy_alignments" falsevalue="" display="checkboxes" label="Save memory on large gappy alignments"
-                    help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments. (-U)" optional="True" />
-                <param name="disable_rate_heterogeneity" type="boolean" checked="no" truevalue="--disable_raite_heterogeneity" falsevalue="" display="checkboxes" label="Disable rate heterogeneity" help="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead. Only works if you specify the CAT model of rate heterogeneity. (_V)" optional="True" />
-                <param name="sliding_window_size" type="integer" value="" label="Sliding window size" optional="True"
-                    help="Sliding window size for leave-one-out site-specific placement bias algorithm. Only effective when used in combination with '-f S'. Default is '100 sites' (-W)" />
-                <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="--parsimony_starting_tree_only" falsevalue="" display="checkboxes"
-                    label="Compute a randomized parsimony starting tree only" optional="True"
-                    help="If you want to only compute a parsimony starting tree with RAxML specify '-y'. The program will exit after computation of the starting tree." />
-                <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file"
-                    help="Specify the file name of a file containing multiple trees e.g. from a bootstrap that shall be used to draw bipartition values onto a tree provided with '-t', It can also be used to compute per site log likelihoods in combination with '-f g' and to read a bunch of trees for '-f h', '-f m' and '-f n'. (-z)" optional="True" />
-                <param name="random_seed" type="integer" value="1234567890" label="Random
-                    seed used for the parsimony inferences" help="(--random_seed)"/>
+                <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 '()&lt;&gt;[]{}' 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>
diff -r 6805e85573b8 -r ba29b5e2a4be tool_dependencies.xml
--- 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>