raxml: raxml.xml annotate

annotate raxml.xml @ 1:ba29b5e2a4be draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raxml commit b23553a3d29d50e05d8b37a5c5780e3ffc937069

author	iuc
date	Tue, 27 Jun 2017 16:27:39 -0400
parents	6805e85573b8
children	a4b71be30c3c

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

Mercurial > repos > iuc > raxml

annotate raxml.xml @ 1:ba29b5e2a4be draft