annotate raxml.xml @ 2:a4b71be30c3c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
author iuc
date Mon, 02 Dec 2019 07:52:10 -0500
parents ba29b5e2a4be
children 14eb2acf30e3
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a4b71be30c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
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1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="8.2.4+galaxy1">
0
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2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
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3 <requirements>
1
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4 <requirement type="package" version="8.2.4">raxml</requirement>
2
a4b71be30c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
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5 <requirement type="package" version="3.6">python</requirement>
0
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6 </requirements>
1
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7 <command detect_errors="exit_code"><![CDATA[
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8 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
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9 #set $slots = $getVar('GALAXY_SLOTS', 1)
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10 #if $slots == 1:
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11 raxmlHPC
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12 ## Cannot have -T 1
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13 #else:
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14 raxmlHPC-PTHREADS
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15 -T $slots
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16 #end if
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17 -s '$infile'
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18 -n galaxy
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19 #if $search_model_selector.model_type == 'aminoacid':
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20 -m ${search_model_selector.base_model}${search_model_selector.aa_search_matrix}${search_model_selector.aa_model_empirical_base_frequencies}
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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21 #else:
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22 -m $search_model_selector.base_model
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23 #end if
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24 -p $random_seed
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25
1
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26 #if $selExtraOpts.extraOptions == 'full':
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27 #if $selExtraOpts.number_of_runs_conditional.number_of_runs_selector == 'by_number_of_runs':
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28 -N $selExtraOpts.number_of_runs_conditional.number_of_runs
0
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29 #else:
1
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30 -N $selExtraOpts.number_of_runs_conditional.number_of_runs_bootstop
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31 #end if
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32 #if $selExtraOpts.weightfile:
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33 -a '$selExtraOpts.weightfile'
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34 #end if
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35 #if $selExtraOpts.secondary_structure_model:
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36 -A $selExtraOpts.secondary_structure_model
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37 #end if
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38 #if str($selExtraOpts.bootseed):
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39 -b $selExtraOpts.bootseed
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40 #end if
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41 -B $selExtraOpts.cutoff_threshold
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42 -c $selExtraOpts.numofcats
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43 $selExtraOpts.search_complete_random_tree
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44 $selExtraOpts.ml_search_convergence
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45 #if $selExtraOpts.model_opt_precision:
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46 -e $selExtraOpts.model_opt_precision
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47 #end if
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48 #if $selExtraOpts.excludefile:
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49 -E '$selExtraOpts.excludefile'
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50 #end if
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51 #if $selExtraOpts.search_algorithm:
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52 -f $selExtraOpts.search_algorithm
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53 #end if
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54 $selExtraOpts.save_memory_cat_model
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55 #if $selExtraOpts.groupingfile:
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56 -g '$selExtraOpts.groupingfile'
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57 #end if
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58 #if $selExtraOpts.enable_evol_heuristics:
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59 -G $selExtraOpts.enable_evol_heuristics
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60 #end if
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61 #if str($selExtraOpts.initial_rearrangement_setting):
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62 -i $selExtraOpts.initial_rearrangement_setting
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63 #end if
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64 #if $selExtraOpts.posterior_bootstopping_analysis:
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65 -I $selExtraOpts.posterior_bootstopping_analysis
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66 #end if
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67 #if $selExtraOpts.majority_rule_consensus:
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68 -J $selExtraOpts.majority_rule_consensus
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69 #end if
1
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70 $selExtraOpts.print_branch_lengths
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71 -K $selExtraOpts.multistate_sub_model
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72 $selExtraOpts.estimate_individual_branch_lengths
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73 #if $selExtraOpts.outgroup_name:
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74 -o '$selExtraOpts.outgroup_name'
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75 #end if
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76 $selExtraOpts.disable_undetermined_seq_check
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77 #if $selExtraOpts.external_protein_model:
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78 -P '$selExtraOpts.external_protein_model'
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79 #end if
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80 #if $selExtraOpts.multiple_model:
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81 -q '$selExtraOpts.multiple_model'
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82 #end if
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83 #if $selExtraOpts.constraint_file:
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84 -r '$selExtraOpts.constraint_file'
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diff changeset
85 #end if
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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86 #if $selExtraOpts.bin_model_parameter_file:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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diff changeset
87 -R '$selExtraOpts.bin_model_parameter_file'
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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88 #end if
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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parents: 0
diff changeset
89 #if $selExtraOpts.secondary_structure_file:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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diff changeset
90 -S '$selExtraOpts.secondary_structure_file'
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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parents: 0
diff changeset
91 #end if
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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parents: 0
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92 #if $selExtraOpts.start_tree_file:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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diff changeset
93 -t '$selExtraOpts.start_tree_file'
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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94 #end if
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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diff changeset
95 $selExtraOpts.use_median_approximation
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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96 $selExtraOpts.save_memory_gappy_alignments
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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97 $selExtraOpts.disable_rate_heterogeneity
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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98 -W $selExtraOpts.sliding_window_size
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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99 #if str($selExtraOpts.rapid_bootstrap_random_seed):
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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100 -x $selExtraOpts.rapid_bootstrap_random_seed
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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101 #end if
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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102 $selExtraOpts.parsimony_starting_tree_only
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103 #end if
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104 && python '$__tool_directory__/raxml.py'
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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105 #if $selExtraOpts.extraOptions == 'full':
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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106 #if str($selExtraOpts.bootseed):
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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107 --bootseed $selExtraOpts.bootseed
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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108 #end if
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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109 #if str($selExtraOpts.rapid_bootstrap_random_seed):
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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110 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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111 #end if
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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112 #if $selExtraOpts.number_of_runs_conditional.number_of_runs_selector == 'by_number_of_runs':
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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113 --number_of_runs $selExtraOpts.number_of_runs_conditional.number_of_runs
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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114 #end if
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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115 #if $selExtraOpts.multiple_model:
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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116 --multiple_model '$selExtraOpts.multiple_model'
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117 #end if
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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118 #end if
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119 ]]></command>
0
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120 <inputs>
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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121 <param name="infile" argument="-s" type="data" format="fasta,phylip" label="Source file" />
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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122 <conditional name="search_model_selector">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
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123 <param name="model_type" type="select" label="Model type">
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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124 <option value="nucleotide" selected="true">Nucleotide</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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125 <option value="aminoacid">Amino Acid</option>
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126 <option value="binary">Binary</option>
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127 <option value="multistate">Multistate</option>
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128 </param>
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129 <when value="nucleotide">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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130 <param name="base_model" type="select" label="Substitution model">
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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131 <option value="GTRCAT">GTRCAT</option>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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132 <option value="GTRCATI">GTRCATI</option>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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133 <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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134 <option value="GTRGAMMAI">GTRGAMMAI</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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135 </param>
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iuc
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136 </when>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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137 <when value="aminoacid">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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138 <param name="base_model" type="select" label="Substitution model">
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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139 <option value="PROTCAT" selected="true">PROTCAT</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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140 <option value="PROTCATI">PROTCATI</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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141 <option value="PROTGAMMA">PROTGAMMA</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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142 <option value="PROTGAMMAI">PROTGAMMAI</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
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143 </param>
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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144 <param name="aa_search_matrix" type="select" label="Matrix">
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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145 <option value="DAYHOFF" selected="true">DAYHOFF</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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146 <option value="DCMUT">DCMUT</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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147 <option value="JTT">JTT</option>
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148 <option value="MTREV">MTREV</option>
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149 <option value="WAG">WAG</option>
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150 <option value="RTREV">RTREV</option>
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151 <option value="CPREV">CPREV</option>
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152 <option value="VT">VT</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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153 <option value="BLOSUM62">BLOSUM62</option>
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154 <option value="MTMAM">MTMAM</option>
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155 <option value="LG">LG</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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156 <option value="MTART">MTART</option>
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iuc
parents:
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157 <option value="MTZOA">MTZOA</option>
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iuc
parents:
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158 <option value="PMB">PMB</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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159 <option value="HIVB">HIVB</option>
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parents:
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160 <option value="HIVW">HIVW</option>
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iuc
parents:
diff changeset
161 <option value="JTTDCMUT">JTTDCMUT</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff changeset
162 <option value="FLU">FLU</option>
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parents:
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163 <option value="DUMMY">DUMMY</option>
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iuc
parents:
diff changeset
164 <option value="DUMMY2">DUMMY2</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
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165 <option value="GTR_UNLINKED">GTR_UNLINKED</option>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
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parents:
diff changeset
166 <option value="GTR">GTR</option>
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iuc
parents:
diff changeset
167 </param>
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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parents: 0
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168 <param name="aa_model_empirical_base_frequencies" type="boolean" truevalue="F" falsevalue="" checked="no" display="checkboxes" label="Use empirical base frequencies in AA models" />
0
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iuc
parents:
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169 </when>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
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170 <when value="binary">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
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171 <param name="base_model" type="select" label="Substitution model">
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
172 <option value="BINCAT">BINCAT</option>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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parents: 0
diff changeset
173 <option value="BINCATI">BINCATI</option>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
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parents: 0
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174 <option value="BINGAMMA">BINGAMMA</option>
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175 <option value="BINGAMMAI">BINGAMMAI</option>
0
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176 </param>
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177 </when>
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178 <when value="multistate">
1
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179 <param name="base_model" type="select" label="Substitution model">
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180 <option value="MULTICAT">MULTICAT</option>
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181 <option value="MULTICATI">MULTICATI</option>
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182 <option value="MULTIGAMMA">MULTIGAMMA</option>
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183 <option value="MULTIGAMMAI">MULTIGAMMAI</option>
0
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184 </param>
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185 </when>
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186 </conditional>
1
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187 <param name="random_seed" argument="-p" type="integer" value="1234567890" label="Random seed used for the parsimony inferences" />
0
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188 <conditional name="selExtraOpts">
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189 <param name="extraOptions" type="select" label="RAxML options to use"
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190 help="The required minimal settings are the input file and the
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191 substitution model. To specify extra options select the 'Full option list'">
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192 <option value="required">Required options only</option>
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193 <option value="full">Full option list</option>
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194 </param>
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195 <when value="required" />
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196 <when value="full">
1
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197 <conditional name="number_of_runs_conditional">
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198 <param name="number_of_runs_selector" type="select" label="Multiple boostrap specification">
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199 <option value="by_number_of_runs">By number of runs</option>
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200 <option value="by_bootstopping">By bootstopping criteria</option>
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201 </param>
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202 <when value="by_number_of_runs">
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203 <param name="number_of_runs" argument="-N" type="integer" value="1" label="Number of alternative runs on distinct starting trees"
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204 help="In combination with the '-b' option, this will invoke a multiple boostrap analysis" />
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205 </when>
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206 <when value="by_bootstopping">
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207 <param name="number_of_runs_bootstop" argument="-N" type="select" label="Bootstopping criteria" help="Bootstopping will only work in combination with '-x' or '-b'">
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208 <option value="autoMR">autoMR</option>
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209 <option value="autoMRE">autoMRE</option>
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210 <option value="autoMRE_IGN">autoMRE_IGN</option>
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211 <option value="autoFC">autoFC</option>
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212 </param>
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213 </when>
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214 </conditional>
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215 <param name="weightfile" argument="-a" type="data" format="txt" optional="true" label="Column weight file" />
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216 <param name="secondary_structure_model" argument="-A" type="select" optional="true" label="Secondary structure substitution model">
0
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217 <option value="S6A">S6A</option>
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218 <option value="S6B">S6B</option>
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219 <option value="S6C">S6C</option>
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220 <option value="S6D">S6D</option>
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221 <option value="S6E">S6E</option>
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222 <option value="S7A">S7A</option>
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223 <option value="S7B">S7B</option>
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224 <option value="S7C">S7C</option>
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225 <option value="S7D">S7D</option>
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226 <option value="S7E">S7E</option>
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227 <option value="S7F">S7F</option>
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228 <option value="S16">S16</option>
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229 <option value="S16A">S16A</option>
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230 <option value="S16B">S16B</option>
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231 </param>
1
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232 <param name="bootseed" argument="-b" type="integer" value="" optional="true" label="Random seed for non-parametric bootstrapping"
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233 help="Specifying a value turns on bootstrapping" />
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234 <param name="rapid_bootstrap_random_seed" argument="-x" type="integer" value="" optional="true" label="Random seed for rapid bootstrapping"
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235 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" />
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236 <param name="cutoff_threshold" argument="-B" type="float" value="0.03" min="0" max="1" label="MR cutoff threshold"
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237 help="Cutoff threshold for the MR-based bootstopping criteria" />
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238 <param name="numofcats" argument="-c" type="integer" value="25" label="Number of Rate Categories for GTRCAT/GTRMIX" />
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239 <!-- (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now. -->
1
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240 <param name="search_complete_random_tree" argument="-d" type="boolean" truevalue="-d" falsevalue=""
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241 label="Start ML optimization from a complete random starting tree" />
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242 <param name="ml_search_convergence" argument="-D" type="boolean" truevalue="-D" falsevalue=""
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243 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" />
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244 <param name="model_opt_precision" argument="-e" type="float" label="Model optimization precision" value="" optional="true"
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245 help="Set model optimization precision in log likelihood units for final optimization of tree topology" />
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246 <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" />
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247 <param name="search_algorithm" argument="-f" type="select" label="Algorithm to execute" optional="true">
0
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248 <option value="a">Rapid bootstrap and best ML tree search (a)</option>
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249 <option value="A">Compute marginal ancestral states (A)</option>
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250 <option value="b">Draw bipartition information (b)</option>
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251 <option value="c">Check if the alignment can be read (c)</option>
1
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252 <option value="d" selected="true">New rapid hill-climbing (d)</option>
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253 <option value="D">Rapid hill-climbing with RELL bootstraps (D)</option>
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254 <option value="e">Optimize model+branch lengths under GAMMA/GAMMAI only (e)</option>
0
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255 <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
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256 <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
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257 <option value="j">Generate bootstrapped alignment files (j)</option>
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258 <option value="J">Compute SH-like support values for the -t tree (J)</option>
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259 <option value="m">Compare bipartitions between -t and -z trees (m)</option>
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260 <option value="n">Compute log likelihood score for -z trees (n)</option>
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261 <option value="o">Use old slower search algorithm (o)</option>
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262 <option value="p">Stepwise MP addition of new sequences (p)</option>
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263 <option value="q">Fast quartet calculator (q)</option>
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264 <option value="r">Compute pairwise RF distances in -z trees (r)</option>
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265 <option value="s">Split a multi-gene alignment (s)</option>
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266 <option value="S">Compute site-specific placement bias (S)</option>
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267 <option value="t">Randomized tree searches on a fixed starting tree (t)</option>
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268 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option>
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269 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option>
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270 <option value="v">Classify environmental sequences (v)</option>
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271 <option value="w">Compute ELW-test on -z trees (w)</option>
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272 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
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273 <option value="y">Classify environmental sequences into a reference tree (y)</option>
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274 </param>
1
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275 <param name="save_memory_cat_model" argument="-F" type="boolean" truevalue="-F" falsevalue=""
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276 label="ML tree searches under CAT model"
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277 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" />
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278 <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" />
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279 <param name="enable_evol_heuristics" argument="-G" type="float" min="0.0" max="1.0" optional="true"
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280 label="Enable the ML-based evolutionary placement algorithm heuristics"
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281 help="By specifying a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML)" />
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282 <param name="initial_rearrangement_setting" argument="-i" type="integer" value="" optional="true" label="Initial rearrangement setting for the subsequent application of topological changes phase" />
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283 <param name="posterior_bootstopping_analysis" argument="-I" type="select" optional="true" label="A posteriori bootstopping analysis">
0
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284 <option value="autoFC">Frequency-based criterion (autoFC)</option>
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285 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option>
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286 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option>
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287 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option>
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288 </param>
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289 <!-- (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy -->
1
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290 <param name="majority_rule_consensus" argument="-J" type="select" optional="true" label="Compute consensus tree">
0
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291 <option value="MR">Majority-rule consensus tree (MR)</option>
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292 <option value="MRE">Extended majority-rule consensus tree (MRE)</option>
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293 <option value="STRICT">Strict consensus tree (STRICT)</option>
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294 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option>
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295 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option>
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296 </param>
1
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297 <param name="print_branch_lengths" argument="-k" type="boolean" truevalue="-k" falsevalue=""
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298 label="Print bootstrapped trees with branch lengths"
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299 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" />
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300 <param name="multistate_sub_model" argument="-K" type="select" label="Specify a multi-state substitution model">
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301 <option value="GTR" selected="true">GTR</option>
0
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302 <option value="ORDERED">ORDERED</option>
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303 <option value="MK">MK</option>
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304 </param>
1
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305 <param name="estimate_individual_branch_lengths" argument="-M" type="boolean" truevalue="-M" falsevalue=""
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306 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" />
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307 <param name="outgroup_name" argument="-o" type="text" value="" optional="true" label="Outgroup name"
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308 help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed" />
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309 <param name="disable_undetermined_seq_check" argument="-O" type="boolean" truevalue="-O" falsevalue=""
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310 label="Disable check for completely undetermined sequence in alignment"
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311 help="The program will not exit with an error message when '-O' is specified." />
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312 <param name="external_protein_model" argument="-P" type="data" format="txt" optional="true" label="External AA (Protein) substitution model"
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313 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" />
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314 <param name="multiple_model" argument="-q" type="data" format="txt" optional="true"
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315 label="Assignment of models to alignment partitions for multiple models of substitution"
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316 help="For the syntax of this file please consult the RaXML manual" />
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317 <param name="constraint_file" argument="-r" type="data" format="txt" optional="true" label="Binary constraint tree"
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318 help="This tree does not need to be comprehensive, i.e. does not have to contain all taxa" />
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319 <param name="bin_model_parameter_file" argument="-R" type="data" format="txt" optional="true" label="Binary model parameter file"
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320 help="This parameter file can be generated with RAxML using the '-f e' tree evaluation option" />
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321 <param name="secondary_structure_file" argument="-S" type="data" format="txt" optional="true" label="Secondary structure file"
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322 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" />
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323 <param name="start_tree_file" argument="-t" type="data" format="nhx" optional="true" label="Starting tree file" help="In Newick format" />
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324 <param name="use_median_approximation" argument="-u" type="boolean" truevalue="-u" falsevalue=""
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325 label="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity" />
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326 <param name="save_memory_gappy_alignments" argument="-U" type="boolean" truevalue="-U" falsevalue=""
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327 label="Save memory on large gappy alignments"
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328 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" />
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329 <param name="disable_rate_heterogeneity" argument="-V" type="boolean" truevalue="-V" falsevalue=""
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330 label="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead"
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331 help="Only works if you specify the CAT model of rate heterogeneity" />
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332 <param name="sliding_window_size" argument="-W" type="integer" min="1" value="100"
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333 label="Sliding window size for leave-one-out site-specific placement bias algorithm"
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334 help="Only effective when used in combination with '-f S'" />
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335 <param name="parsimony_starting_tree_only" argument="-y" type="boolean" truevalue="-y" falsevalue=""
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336 label="Compute a randomized parsimony starting tree only"
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337 help="The program will exit after computation of the starting tree" />
0
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338 </when>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
339 </conditional>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
340 </inputs>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
341 <outputs>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
342 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
343 <!-- REQUIRED -->
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
344 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
345 <filter>selExtraOpts['extraOptions'] == 'required'</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
346 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
347 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
348 <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
349 <filter>selExtraOpts['extraOptions'] == 'required'</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
350 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
351 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
352 <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
353 <filter>selExtraOpts['extraOptions'] == 'required'</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
354 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
355 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
356 <!-- ADVANCED -->
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
357 <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
358 <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
359 <filter>selExtraOpts['extraOptions'] == "full"</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
360 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
361 <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
362 <!-- <filter>selExtraOpts['extraOptions'] == 'full'</filter> -->
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
363 <!-- <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
364 <filter>not selExtraOpts['majority_rule_consensus']</filter> -->
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
365 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
366 <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
367 <filter>selExtraOpts['extraOptions'] == "full"</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
368 <filter>selExtraOpts['multiple_model'] != ''</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
369 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
370 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
371 <filter>selExtraOpts['extraOptions'] == "full"</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
372 <filter>selExtraOpts['multiple_model'] is not None </filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
373 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
374 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
375 <filter>selExtraOpts['extraOptions'] == "full"</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
376 <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
377 <filter>selExtraOpts['bootseed'] == ''</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
378 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
379 <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
380 <filter>not selExtraOpts['majority_rule_consensus']</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
381 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
382 <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
383 <filter>selExtraOpts['extraOptions'] == "full"</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
384 <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
385 <filter>selExtraOpts['bootseed'] == ''</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
386 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
387 <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
388 <filter>not selExtraOpts['majority_rule_consensus']</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
389 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
390 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
391 <filter>selExtraOpts['extraOptions'] == "full"</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
392 <filter>selExtraOpts['multiple_model'] is not None</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
393 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
394 <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
395 <filter>selExtraOpts['extraOptions'] == "full"</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
396 <!--
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
397 <filter>selExtraOpts['rapid_bootstrap_random_seed'] == ''</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
398 <filter>selExtraOpts['bootseed'] == ''</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
399 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
400 <filter>selExtraOpts['constraint_file'] is None</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
401 <filter>selExtraOpts['groupingfile'] is None</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
402 <filter>selExtraOpts['search_complete_random_tree'] is False</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
403 <filter>selExtraOpts['start_tree_file'] is None</filter>
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
404 <filter>not selExtraOpts['majority_rule_consensus'] == ''</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
405 -->
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
406 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
407 <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
408 <filter>selExtraOpts['extraOptions'] == "full"</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
409 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
410 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
411 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
412 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions">
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
413 <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
414 <filter>selExtraOpts['extraOptions'] == "full"</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
415 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
416 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels">
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
417 <filter>selExtraOpts['extraOptions'] == "full"</filter>
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
418 <filter>selExtraOpts['search_algorithm'] == 'b' or (selExtraOpts['search_algorithm'] == 'a' and selExtraOpts['rapid_bootstrap_random_seed'] != '') </filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
419 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
420 <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
421 <filter>selExtraOpts['extraOptions'] == "full"</filter>
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
422 <filter>selExtraOpts['majority_rule_consensus'] == 'STRICT'</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
423 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
424 <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
425 <filter>selExtraOpts['extraOptions'] == "full"</filter>
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
426 <filter>selExtraOpts['majority_rule_consensus'] == 'MR'</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
427 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
428 <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
429 <filter>selExtraOpts['extraOptions'] == "full"</filter>
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
430 <filter>selExtraOpts['majority_rule_consensus'] == 'MRE'</filter>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
431 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
432 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences.">
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
433 <filter>selExtraOpts['search_algorithm'] == 'm' </filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
434 <filter>selExtraOpts['extraOptions'] == "full"</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
435 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
436 <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores">
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
437 <filter>selExtraOpts['search_algorithm'] == 'g' </filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
438 <filter>selExtraOpts['extraOptions'] == "full"</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
439 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
440 <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances">
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
441 <filter>selExtraOpts['search_algorithm'] == 'x' </filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
442 <filter>selExtraOpts['extraOptions'] == "full"</filter>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
443 </data>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
444 </outputs>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
445 <tests>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
446 <test>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
447 <param name="extraOptions" value="required"/>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
448 <param name="infile" value="dna.phy"/>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
449 <param name="model_type" value="nucleotide"/>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
450 <param name="base_model" value="GTRCAT"/>
2
a4b71be30c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
iuc
parents: 1
diff changeset
451 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" ftype="nhx" />
a4b71be30c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
iuc
parents: 1
diff changeset
452 <output name="bestTree" ftype="nhx">
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
453 <assert_contents>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
454 <has_text_matching expression="Frog" />
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
455 </assert_contents>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
456 </output>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
457 </test>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
458 <test>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
459 <param name="extraOptions" value="full"/>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
460 <param name="infile" value="dna.fasta"/>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
461 <param name="model_type" value="nucleotide"/>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
462 <param name="base_model" value="GTRCAT"/>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
463 <param name="number_of_runs" value="5"/>
2
a4b71be30c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
iuc
parents: 1
diff changeset
464 <output name="parsimonyTree" ftype="nhx">
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
465 <assert_contents>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
466 <has_text_matching expression="Chicken" />
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
467 </assert_contents>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
468 </output>
2
a4b71be30c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
iuc
parents: 1
diff changeset
469 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.multi" ftype="nhx"/>
a4b71be30c3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit 9f9e37b75ae2e5735289eeec1c74ff49e6e388e0"
iuc
parents: 1
diff changeset
470 <output name="bestTree" ftype="nhx">
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
471 <assert_contents>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
472 <has_text_matching expression="Whale" />
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
473 </assert_contents>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
474 </output>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
475 </test>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
476 </tests>
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
477 <help><![CDATA[
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
478 RAxML_ (Randomized Axelerated Maximum Likelihood) is a program for Maximum Likelihood-based inference of large phylogenetic
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
479 trees. The program is explicitly being developed to efficiently infer trees for
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
480 extremely large datasets, either in terms of the number of taxa and/or the
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
481 sequence length.
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
482
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
483 .. _RAxML: http://www.exelixis-lab.org/web/software/raxml/
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
484
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
485 **Tool development**:
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
486
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
487 Oleksandr Moskalenko with adaptations from Tiago Antao.
1
ba29b5e2a4be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069
iuc
parents: 0
diff changeset
488 ]]></help>
0
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
489 <citations>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
490 <citation type="doi">10.1093/bioinformatics/btu033</citation>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
491 </citations>
6805e85573b8 planemo upload for repository https://github.com/stamatak/standard-RAxML commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
iuc
parents:
diff changeset
492 </tool>