raxml: raxml.xml annotate

annotate raxml.xml @ 55:730aff7a4ae5 draft default tip

planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty

author	tiagoantao
date	Sun, 22 Nov 2015 15:46:25 -0500
parents	6e672cd847df
children

rev	line source
0 96915eee708d Uploaded tiagoantao parents: diff changeset	1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1">
15 ac873ecba2e8 planemo upload commit 6d4b6d49afc22782142019d31fc335d7d542b307 tiagoantao parents: 11 diff changeset	2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
0 96915eee708d Uploaded tiagoantao parents: diff changeset	3 <requirements>
3 b4ed83696908 planemo upload commit 3ac7fc026930ed9a7951e0a937c16d2af2f1499a-dirty tiagoantao parents: 0 diff changeset	4 <requirement type='package' version="8.2.4">raxml</requirement>
0 96915eee708d Uploaded tiagoantao parents: diff changeset	5 </requirements>
96915eee708d Uploaded tiagoantao parents: diff changeset	6 <command interpreter="python">raxml.py
96915eee708d Uploaded tiagoantao parents: diff changeset	7 ## Required parameters
33 d2a97acb9cfc planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 32 diff changeset	8 ## binary is hard-coded to the pthreads enabled raxml executable if threads > 1
0 96915eee708d Uploaded tiagoantao parents: diff changeset	9 ## (-T)
31 b208b2d8148d planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 30 diff changeset	10 ## Cannot have --threads 1
41 9b315740c5e8 planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 40 diff changeset	11 #set $slots = $getVar('GALAXY_SLOTS', 1)
40 7f7a15dc5b83 planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 39 diff changeset	12 #if $slots == 1:
33 d2a97acb9cfc planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 32 diff changeset	13 --binary "raxmlHPC"
39 263441e91fbd planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 38 diff changeset	14 --threads 1
38 2d72690325cf planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 37 diff changeset	15 #else:
33 d2a97acb9cfc planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 32 diff changeset	16 --binary "raxmlHPC-PTHREADS"
40 7f7a15dc5b83 planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 39 diff changeset	17 --threads $slots
25 2d9f1ef9b5cc planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 24 diff changeset	18 #end if
0 96915eee708d Uploaded tiagoantao parents: diff changeset	19 ## (-s)
96915eee708d Uploaded tiagoantao parents: diff changeset	20 --source $infile
96915eee708d Uploaded tiagoantao parents: diff changeset	21 ## (-m)
96915eee708d Uploaded tiagoantao parents: diff changeset	22 --model_type $search_model_selector.model_type
96915eee708d Uploaded tiagoantao parents: diff changeset	23 --base_model $search_model_selector.base_model
96915eee708d Uploaded tiagoantao parents: diff changeset	24 #if str( $search_model_selector.model_type ) == 'aminoacid':
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	25 $search_model_selector.aa_model_empirical_base_frequencies
0 96915eee708d Uploaded tiagoantao parents: diff changeset	26 #if $search_model_selector.aa_search_matrix:
96915eee708d Uploaded tiagoantao parents: diff changeset	27 --aa_search_matrix $search_model_selector.aa_search_matrix
96915eee708d Uploaded tiagoantao parents: diff changeset	28 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	29 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	30 ## (-p)
96915eee708d Uploaded tiagoantao parents: diff changeset	31 #if $random_seed:
96915eee708d Uploaded tiagoantao parents: diff changeset	32 --random_seed $random_seed
96915eee708d Uploaded tiagoantao parents: diff changeset	33 #else
96915eee708d Uploaded tiagoantao parents: diff changeset	34 --random_seed 1234567890
96915eee708d Uploaded tiagoantao parents: diff changeset	35 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	36
96915eee708d Uploaded tiagoantao parents: diff changeset	37 ## Optional parameters
96915eee708d Uploaded tiagoantao parents: diff changeset	38
96915eee708d Uploaded tiagoantao parents: diff changeset	39 #if str( $selExtraOpts.extraOptions ) == 'full':
96915eee708d Uploaded tiagoantao parents: diff changeset	40 ## (-N/#)
96915eee708d Uploaded tiagoantao parents: diff changeset	41 #if $selExtraOpts.number_of_runs:
96915eee708d Uploaded tiagoantao parents: diff changeset	42 --number_of_runs $selExtraOpts.number_of_runs
96915eee708d Uploaded tiagoantao parents: diff changeset	43 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	44 #if $selExtraOpts.number_of_runs_bootstop:
96915eee708d Uploaded tiagoantao parents: diff changeset	45 --number_of_runs_bootstop $selExtraOpts.number_of_runs_bootstop
96915eee708d Uploaded tiagoantao parents: diff changeset	46 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	47 ## (-a)
96915eee708d Uploaded tiagoantao parents: diff changeset	48 #if $selExtraOpts.weightfile:
96915eee708d Uploaded tiagoantao parents: diff changeset	49 --weightfile $selExtraOpts.weightfile
96915eee708d Uploaded tiagoantao parents: diff changeset	50 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	51 ## (-b)
96915eee708d Uploaded tiagoantao parents: diff changeset	52 #if str ($selExtraOpts.secondary_structure_model) != "":
96915eee708d Uploaded tiagoantao parents: diff changeset	53 --secondary_structure_model $selExtraOpts.secondary_structure_model
96915eee708d Uploaded tiagoantao parents: diff changeset	54 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	55 ## (-b)
96915eee708d Uploaded tiagoantao parents: diff changeset	56 #if $selExtraOpts.bootseed:
96915eee708d Uploaded tiagoantao parents: diff changeset	57 --bootseed $selExtraOpts.bootseed
96915eee708d Uploaded tiagoantao parents: diff changeset	58 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	59 ## (-c)
96915eee708d Uploaded tiagoantao parents: diff changeset	60 #if $selExtraOpts.numofcats:
96915eee708d Uploaded tiagoantao parents: diff changeset	61 --numofcats $selExtraOpts.numofcats
96915eee708d Uploaded tiagoantao parents: diff changeset	62 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	63 ## (-d)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	64 $selExtraOpts.search_complete_random_tree
0 96915eee708d Uploaded tiagoantao parents: diff changeset	65 ## (-D)
21 48526baa210f planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501-dirty tiagoantao parents: 20 diff changeset	66 $selExtraOpts.ml_search_convergence
0 96915eee708d Uploaded tiagoantao parents: diff changeset	67 ## (-e)
96915eee708d Uploaded tiagoantao parents: diff changeset	68 #if $selExtraOpts.model_opt_precision:
96915eee708d Uploaded tiagoantao parents: diff changeset	69 --model_opt_precision $selExtraOpts.model_opt_precision
96915eee708d Uploaded tiagoantao parents: diff changeset	70 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	71 ## (-E)
96915eee708d Uploaded tiagoantao parents: diff changeset	72 #if $selExtraOpts.excludefile:
96915eee708d Uploaded tiagoantao parents: diff changeset	73 --excludefile $selExtraOpts.excludefile
96915eee708d Uploaded tiagoantao parents: diff changeset	74 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	75 ## (-f)
96915eee708d Uploaded tiagoantao parents: diff changeset	76 #if $selExtraOpts.search_algorithm:
96915eee708d Uploaded tiagoantao parents: diff changeset	77 --search_algorithm $selExtraOpts.search_algorithm
96915eee708d Uploaded tiagoantao parents: diff changeset	78 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	79 ## (-F)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	80 $selExtraOpts.save_memory_cat_model
0 96915eee708d Uploaded tiagoantao parents: diff changeset	81 ## (-g)
96915eee708d Uploaded tiagoantao parents: diff changeset	82 #if $selExtraOpts.groupingfile:
96915eee708d Uploaded tiagoantao parents: diff changeset	83 --groupingfile $selExtraOpts.groupingfile
96915eee708d Uploaded tiagoantao parents: diff changeset	84 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	85 ## (-G)
96915eee708d Uploaded tiagoantao parents: diff changeset	86 #if $selExtraOpts.enable_evol_heuristics:
96915eee708d Uploaded tiagoantao parents: diff changeset	87 --enable_evol_heuristics $selExtraOpts.enable_evol_heuristics
96915eee708d Uploaded tiagoantao parents: diff changeset	88 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	89 ## (-i)
96915eee708d Uploaded tiagoantao parents: diff changeset	90 #if $selExtraOpts.initial_rearrangement_setting:
96915eee708d Uploaded tiagoantao parents: diff changeset	91 --initial_rearrangement_setting $selExtraOpts.initial_rearrangement_setting
96915eee708d Uploaded tiagoantao parents: diff changeset	92 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	93 ## (-I)
96915eee708d Uploaded tiagoantao parents: diff changeset	94 #if $selExtraOpts.posterior_bootstopping_analysis:
96915eee708d Uploaded tiagoantao parents: diff changeset	95 --posterior_bootstopping_analysis $selExtraOpts.posterior_bootstopping_analysis
96915eee708d Uploaded tiagoantao parents: diff changeset	96 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	97 ## (-J)
96915eee708d Uploaded tiagoantao parents: diff changeset	98 #if $selExtraOpts.majority_rule_consensus:
96915eee708d Uploaded tiagoantao parents: diff changeset	99 --majority_rule_consensus $selExtraOpts.majority_rule_consensus
96915eee708d Uploaded tiagoantao parents: diff changeset	100 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	101 ## (-k)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	102 $selExtraOpts.print_branch_lengths
0 96915eee708d Uploaded tiagoantao parents: diff changeset	103 ## (-K)
96915eee708d Uploaded tiagoantao parents: diff changeset	104 #if str ($selExtraOpts.multistate_sub_model) != "":
96915eee708d Uploaded tiagoantao parents: diff changeset	105 --multistate_sub_model $selExtraOpts.multistate_sub_model
96915eee708d Uploaded tiagoantao parents: diff changeset	106 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	107 ## (-m) - see elsewhere
96915eee708d Uploaded tiagoantao parents: diff changeset	108 ## (-M)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	109 $selExtraOpts.estimate_individual_branch_lengths
0 96915eee708d Uploaded tiagoantao parents: diff changeset	110 ## (-n) - see elsewhere
96915eee708d Uploaded tiagoantao parents: diff changeset	111 ## (-o)
96915eee708d Uploaded tiagoantao parents: diff changeset	112 #if $selExtraOpts.outgroup_name:
96915eee708d Uploaded tiagoantao parents: diff changeset	113 --outgroup_name $selExtraOpts.outgroup_name
96915eee708d Uploaded tiagoantao parents: diff changeset	114 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	115 ## (-O)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	116 $selExtraOpts.disable_undetermined_seq_check
0 96915eee708d Uploaded tiagoantao parents: diff changeset	117 ## (-P)
96915eee708d Uploaded tiagoantao parents: diff changeset	118 #if $selExtraOpts.external_protein_model:
96915eee708d Uploaded tiagoantao parents: diff changeset	119 --external_protein_model $selExtraOpts.external_protein_model
96915eee708d Uploaded tiagoantao parents: diff changeset	120 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	121 ## (-q)
96915eee708d Uploaded tiagoantao parents: diff changeset	122 #if $selExtraOpts.multiple_model:
96915eee708d Uploaded tiagoantao parents: diff changeset	123 --multiple_model $selExtraOpts.multiple_model
96915eee708d Uploaded tiagoantao parents: diff changeset	124 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	125 ## (-r)
96915eee708d Uploaded tiagoantao parents: diff changeset	126 #if $selExtraOpts.constraint_file:
96915eee708d Uploaded tiagoantao parents: diff changeset	127 --constraint_file $selExtraOpts.constraint_file
96915eee708d Uploaded tiagoantao parents: diff changeset	128 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	129 ## (-R)
96915eee708d Uploaded tiagoantao parents: diff changeset	130 #if $selExtraOpts.bin_model_parameter_file:
96915eee708d Uploaded tiagoantao parents: diff changeset	131 --bin_model_parameter_file $selExtraOpts.bin_model_parameter_file
96915eee708d Uploaded tiagoantao parents: diff changeset	132 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	133 ## (-S)
96915eee708d Uploaded tiagoantao parents: diff changeset	134 #if $selExtraOpts.secondary_structure_file:
96915eee708d Uploaded tiagoantao parents: diff changeset	135 --secondary_structure_file $selExtraOpts.secondary_structure_file
96915eee708d Uploaded tiagoantao parents: diff changeset	136 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	137 ## (-t)
96915eee708d Uploaded tiagoantao parents: diff changeset	138 #if $selExtraOpts.start_tree_file:
96915eee708d Uploaded tiagoantao parents: diff changeset	139 --starting_tree $selExtraOpts.start_tree_file
96915eee708d Uploaded tiagoantao parents: diff changeset	140 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	141 ## (-T) see elsewhere
96915eee708d Uploaded tiagoantao parents: diff changeset	142 ## (-u)
22 ec5e58cd3a68 planemo upload commit db9228a4b4042ad9493237882a8266529bb69931 tiagoantao parents: 21 diff changeset	143 $selExtraOpts.use_median_approximation
0 96915eee708d Uploaded tiagoantao parents: diff changeset	144 ## (-U)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	145 $selExtraOpts.save_memory_gappy_alignments
0 96915eee708d Uploaded tiagoantao parents: diff changeset	146 ## (-V)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	147 $selExtraOpts.disable_rate_heterogeneity
0 96915eee708d Uploaded tiagoantao parents: diff changeset	148 ## (-W)
96915eee708d Uploaded tiagoantao parents: diff changeset	149 #if $selExtraOpts.sliding_window_size:
96915eee708d Uploaded tiagoantao parents: diff changeset	150 --sliding_window_size $selExtraOpts.sliding_window_size
96915eee708d Uploaded tiagoantao parents: diff changeset	151 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	152 ## (-x)
96915eee708d Uploaded tiagoantao parents: diff changeset	153 #if $selExtraOpts.rapid_bootstrap_random_seed:
96915eee708d Uploaded tiagoantao parents: diff changeset	154 --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed
96915eee708d Uploaded tiagoantao parents: diff changeset	155 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	156 ## (-y)
23 dc9a86a5d97e planemo upload commit db9228a4b4042ad9493237882a8266529bb69931-dirty tiagoantao parents: 22 diff changeset	157 $selExtraOpts.parsimony_starting_tree_only
0 96915eee708d Uploaded tiagoantao parents: diff changeset	158 ## (-z)
96915eee708d Uploaded tiagoantao parents: diff changeset	159 #if $selExtraOpts.file_multiple_trees:
96915eee708d Uploaded tiagoantao parents: diff changeset	160 --file_multiple_trees $selExtraOpts.file_multiple_trees
96915eee708d Uploaded tiagoantao parents: diff changeset	161 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	162 #end if
96915eee708d Uploaded tiagoantao parents: diff changeset	163
96915eee708d Uploaded tiagoantao parents: diff changeset	164 </command>
96915eee708d Uploaded tiagoantao parents: diff changeset	165 <inputs>
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	166 ## (-s)
d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	167 <param type="data" format="fasta,phylip" name="infile" label="Source file"/>
0 96915eee708d Uploaded tiagoantao parents: diff changeset	168 ## (-m)
96915eee708d Uploaded tiagoantao parents: diff changeset	169 <conditional name="search_model_selector">
96915eee708d Uploaded tiagoantao parents: diff changeset	170 <param name="model_type" type="select" label="Model Type">
96915eee708d Uploaded tiagoantao parents: diff changeset	171 <option value="nucleotide" selected="true">Nucleotide</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	172 <option value="aminoacid">Amino Acid</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	173 <option value="binary">Binary</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	174 <option value="multistate">Multistate</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	175 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	176 <when value="nucleotide">
96915eee708d Uploaded tiagoantao parents: diff changeset	177 ## Nucleotide substitution models
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	178 <param name="base_model" type="select" label="Substitution Model">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	179 <option value="GTRCAT">GTRCAT</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	180 <option value="GTRCATI">GTRCATI</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	181 <option value="GTRGAMMA" select="true">GTRGAMMA</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	182 <option value="GTRGAMMAI">GTRGAMMAI</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	183 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	184 </when>
96915eee708d Uploaded tiagoantao parents: diff changeset	185 ## Aminoacid substitution models
96915eee708d Uploaded tiagoantao parents: diff changeset	186 <when value="aminoacid">
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	187 <param name="aa_model_empirical_base_frequencies"
d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	188 type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	189 <param name="base_model" type="select" label="Substitution Model (-m)">
96915eee708d Uploaded tiagoantao parents: diff changeset	190 <option value="PROTCAT" select="true">PROTCAT</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	191 <option value="PROTCATI">PROTCATI</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	192 <option value="PROTGAMMA">PROTGAMMA</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	193 <option value="PROTGAMMAI">PROTGAMMAI</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	194 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	195 <param name="aa_search_matrix" type="select" label="Matrix">
96915eee708d Uploaded tiagoantao parents: diff changeset	196 <option value="DAYHOFF" select="true">DAYHOFF</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	197 <option value="DCMUT">DCMUT</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	198 <option value="JTT">JTT</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	199 <option value="MTREV">MTREV</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	200 <option value="WAG">WAG</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	201 <option value="RTREV">RTREV</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	202 <option value="CPREV">CPREV</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	203 <option value="VT">VT</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	204 <option value="BLOSUM62">BLOSUM62</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	205 <option value="MTMAM">MTMAM</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	206 <option value="LG">LG</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	207 <option value="MTART">MTART</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	208 <option value="MTZOA">MTZOA</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	209 <option value="PMB">PMB</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	210 <option value="HIVB">HIVB</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	211 <option value="HIVW">HIVW</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	212 <option value="JTTDCMUT">JTTDCMUT</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	213 <option value="FLU">FLU</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	214 <option value="DUMMY">DUMMY</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	215 <option value="DUMMY2">DUMMY2</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	216 <option value="GTR_UNLINKED">GTR_UNLINKED</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	217 <option value="GTR">GTR</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	218 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	219 </when>
96915eee708d Uploaded tiagoantao parents: diff changeset	220 ## Binary substitution models
96915eee708d Uploaded tiagoantao parents: diff changeset	221 <when value="binary">
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	222 <param name="base_model" type="select" label="Substitution Model">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	223 <option value="BINCAT">BINCAT</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	224 <option value="BINCATI">BINCATI</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	225 <option value="BINGAMMA">BINGAMMA</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	226 <option value="BINGAMMAI">BINGAMMAI</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	227 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	228 </when>
96915eee708d Uploaded tiagoantao parents: diff changeset	229 ## Multi-state substitution models
96915eee708d Uploaded tiagoantao parents: diff changeset	230 <when value="multistate">
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	231 <param name="base_model" type="select" label="Substitution Model">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	232 <option value="MULTICAT">MULTICAT</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	233 <option value="MULTICATI">MULTICATI</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	234 <option value="MULTIGAMMA">MULTIGAMMA</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	235 <option value="MULTIGAMMAI">MULTIGAMMAI</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	236 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	237 </when>
96915eee708d Uploaded tiagoantao parents: diff changeset	238 </conditional>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	239 <param name="random_seed" type="integer" value="1234567890" label="Random
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	240 seed used for the parsimony inferences" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	241 <conditional name="selExtraOpts">
96915eee708d Uploaded tiagoantao parents: diff changeset	242 <param name="extraOptions" type="select" label="RAxML options to use"
96915eee708d Uploaded tiagoantao parents: diff changeset	243 help="The required minimal settings are the input file and the
96915eee708d Uploaded tiagoantao parents: diff changeset	244 substitution model. To specify extra options select the 'Full option list'">
96915eee708d Uploaded tiagoantao parents: diff changeset	245 <option value="required">Required options only</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	246 <option value="full">Full option list</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	247 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	248 <when value="full">
96915eee708d Uploaded tiagoantao parents: diff changeset	249 ## (-N/#)
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	250 <param name="number_of_runs" type="integer" value=""
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	251 label="Number of runs" help="Specify the number of
d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	252 alternative runs (-N\|#) on distinct starting trees In combination
0 96915eee708d Uploaded tiagoantao parents: diff changeset	253 with the '-b' option will invoke a multiple boostrap analysis.
96915eee708d Uploaded tiagoantao parents: diff changeset	254 You can add the bootstopping criteria by choosing the autoMR,
96915eee708d Uploaded tiagoantao parents: diff changeset	255 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
96915eee708d Uploaded tiagoantao parents: diff changeset	256 providing a number here. Bootstopping will only work in
96915eee708d Uploaded tiagoantao parents: diff changeset	257 combination with '-x' or '-b'."
96915eee708d Uploaded tiagoantao parents: diff changeset	258 optional="True" />
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	259 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	260 <option value="" selected="yes"></option>
96915eee708d Uploaded tiagoantao parents: diff changeset	261 <option value="autoMR">autoMR</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	262 <option value="autoMRE">autoMRE</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	263 <option value="autoMRE_IGN">autoMRE_IGN</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	264 <option value="autoFC">autoFC</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	265 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	266 ## Alphabetical Listing of Advanced Options
96915eee708d Uploaded tiagoantao parents: diff changeset	267 ## (-a)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	268 <param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	269 ## (-A)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	270 <param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	271 <option value="" selected="yes"></option>
96915eee708d Uploaded tiagoantao parents: diff changeset	272 <option value="S6A">S6A</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	273 <option value="S6B">S6B</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	274 <option value="S6C">S6C</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	275 <option value="S6D">S6D</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	276 <option value="S6E">S6E</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	277 <option value="S7A">S7A</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	278 <option value="S7B">S7B</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	279 <option value="S7C">S7C</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	280 <option value="S7D">S7D</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	281 <option value="S7E">S7E</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	282 <option value="S7F">S7F</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	283 <option value="S16">S16</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	284 <option value="S16A">S16A</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	285 <option value="S16B">S16B</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	286 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	287 ## (-b)
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	288 <param name="bootseed" type="integer" value="" label="Random number for non-parametric bootstrapping" refresh_on_change='true' optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	289 ## (-x)
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	290 <param name="rapid_bootstrap_random_seed" type="integer" value='' label="Rapid bootstrapping random seed" optional="True" help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT." />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	291 ## (-B)
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	292 <param name="cutoff_threshold" type="float" label="MR Cutoff threshold" value="" help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1" optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	293 ## (-c)
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	294 <param name="numofcats" type="integer" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	295 ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now.
96915eee708d Uploaded tiagoantao parents: diff changeset	296 ## (-d)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	297 <param name="search_complete_random_tree" type="boolean" checked="False" truevalue="--search_complete_random_tree" falsevalue="" display="checkboxes" label="Start ML optimization from a complete random starting tree" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	298 ## (-D)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	299 <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue="" label="ML search convergence criterion" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	300 ## (-e)
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	301 <param name="model_opt_precision" type="float" label="Model optimization precision" value="" help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used" optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	302 ## (-E)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	303 <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	304 ## (-f)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	305 <param name="search_algorithm" type="select" label="Algorithm to execute" optional="True">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	306 <option value="a">Rapid bootstrap and best ML tree search (a)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	307 <option value="A">Compute marginal ancestral states (A)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	308 <option value="b">Draw bipartition information (b)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	309 <option value="c">Check if the alignment can be read (c)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	310 <option value="d" selected="true">Hill-climbing ML Search (d) (default)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	311 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	312 <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	313 <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	314 <option value="j">Generate bootstrapped alignment files (j)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	315 <option value="J">Compute SH-like support values for the -t tree (J)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	316 <option value="m">Compare bipartitions between -t and -z trees (m)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	317 <option value="n">Compute log likelihood score for -z trees (n)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	318 <option value="o">Use old slower search algorithm (o)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	319 <option value="p">Stepwise MP addition of new sequences (p)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	320 <option value="q">Fast quartet calculator (q)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	321 <option value="r">Compute pairwise RF distances in -z trees (r)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	322 <option value="s">Split a multi-gene alignment (s)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	323 <option value="S">Compute site-specific placement bias (S)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	324 <option value="t">Randomized tree searches on a fixed starting tree (t)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	325 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	326 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	327 <option value="v">Classify environmental sequences (v)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	328 <option value="w">Compute ELW-test on -z trees (w)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	329 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	330 <option value="y">Classify environmental sequences into a reference tree (y)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	331 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	332 ## (-F)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	333 <param name="save_memory_cat_model" type="boolean" checked="no" truevalue="--save_memory_cat_model" falsevalue="" display="checkboxes" label="ML tree searches under CAT model" optional="True" help="ML tree searches under CAT model for very large trees without switching to GAMMA in the end (saves memory) and no thorough optimization under GAMMA" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	334 ## (-g)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	335 <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	336 ## (-G)
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	337 <param name="enable_evol_heuristics" type="float" label="Enable the ML-based evolutionary placement algorithm heuristics" help="Enable the ML-based evolutionary placement algorithm heuristics by specifiyng a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML)." optional="True" >
0 96915eee708d Uploaded tiagoantao parents: diff changeset	338 <validator type="in_range" message="0.0 <= fraction <= 1.0" min="0.0" max="1.0"/>
96915eee708d Uploaded tiagoantao parents: diff changeset	339 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	340 ## (-i)
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	341 <param name="initial_rearrangement_setting" type="integer" value="" label="Initial rearrangement setting" optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	342 ## (-I)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	343 <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	344 <option value="" selected="True"></option>
96915eee708d Uploaded tiagoantao parents: diff changeset	345 <option value="autoFC">Frequency-based criterion (autoFC)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	346 <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	347 <option value="autoMRE">Extended majority-rule consensus tree criterion (autoMRE)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	348 <option value="autoMRE_IGN">Extended MR consensus tree criterion with bipartitions (autoMRE_IGN)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	349 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	350 ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy
96915eee708d Uploaded tiagoantao parents: diff changeset	351 ## (-J)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	352 <param name="majority_rule_consensus" type="select" label="Compute consensus tree" optional="True">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	353 <option value="" selected="True"></option>
96915eee708d Uploaded tiagoantao parents: diff changeset	354 <option value="MR">Majority-rule consensus tree (MR)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	355 <option value="MRE">Extended majority-rule consensus tree (MRE)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	356 <option value="STRICT">Strict consensus tree (STRICT)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	357 <option value="STRICT_DROP">Identify strict dropsets (STRICT_DROP)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	358 <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	359 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	360 ## (-k)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	361 <param name="print_branch_lengths" type="boolean" checked="no" truevalue="--print_branch_lengths" falsevalue="" display="checkboxes" label="Print bootstrapped trees with branch lengths" help="Specifies that bootstrapped trees should be printed with branch lengths. The bootstraps will run a bit longer, because model parameters will be optimized at the end of each run under GAMMA or GAMMA+P-Invar respectively." optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	362 ## (-K)
96915eee708d Uploaded tiagoantao parents: diff changeset	363 <param name="multistate_sub_model" type="select" label="Specify a
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	364 multi-state substitution model" optional="True">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	365 <option value="" selected="true"></option>
96915eee708d Uploaded tiagoantao parents: diff changeset	366 <option value="GTR">GTR</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	367 <option value="ORDERED">ORDERED</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	368 <option value="MK">MK</option>
96915eee708d Uploaded tiagoantao parents: diff changeset	369 </param>
96915eee708d Uploaded tiagoantao parents: diff changeset	370 ## (-M)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	371 <param name="estimate_individual_branch_lengths" type="boolean" checked="no" truevalue="--estimate_individual_branch_lengths" falsevalue="" display="checkboxes" label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file (-q)." optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	372 ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files
96915eee708d Uploaded tiagoantao parents: diff changeset	373 ## (-o)
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	374 <param name="outgroup_name" type="text" value="" label="Outgroup name" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed." optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	375 ## (-O)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	376 <param name="disable_undetermined_seq_check" type="boolean" checked="no" truevalue="--disable_undertermined_seq_check" falsevalue="" display="checkboxes" label="Disable check for completely undetermined sequence in alignment" optional="True" help="Disable the check for completely undetermined sequence in alignment. The program will not exit with an error message when '-O' is specified." />
d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	377 <param name="external_protein_model" format="txt" type="data" label="External AA substitution model" help="Specify the file name of a user-defined AA (Protein) substitution model. This file must contain 420 entries, the first 400 being the AA substitution rates (this must be a symmetric matrix) and the last 20 are the empirical base frequencies." optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	378 ## (-q)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	379 <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" optional="True" help="Specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual." />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	380 ## (-r)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	381 <param name="constraint_file" format="txt" type="data" label="Binary constraint tree" optional="True" help="Specify the file name of a binary constraint tree. This tree does not need to be comprehensive, i.e. must not contain all taxa." />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	382 ## (-R)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	383 <param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file" optional="True" help="Specify the file name of a binary model parameter file that has previously been generated with RAxML using the '-f e' tree evaluation option." />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	384 ## (-s) source file option is in the required options section
96915eee708d Uploaded tiagoantao parents: diff changeset	385 ## (-S)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	386 <param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file" optional="True" help="Specify the name of a secondary structure file. The file can contain '.' for alignment columns that do not form part of a stem and characters '()<>[]{}' to define stem regions and pseudoknots."/>
0 96915eee708d Uploaded tiagoantao parents: diff changeset	387 ## (-t)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	388 <param name="start_tree_file" format="txt" type="data" label="Starting tree file" optional="True" help="Specify a user starting tree file name in Newick format." />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	389 ## (-T) is hard-coded in the required options section
22 ec5e58cd3a68 planemo upload commit db9228a4b4042ad9493237882a8266529bb69931 tiagoantao parents: 21 diff changeset	390 <param name="use_median_approximation" type="boolean" checked="no" truevalue="--use_median_approximation" falsevalue="" display="checkboxes" label="Use the median for the discrete approximation" help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity." optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	391 ## (-U)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	392 <param name="save_memory_gappy_alignments" type="boolean" checked="no" truevalue="--save_memory_gappy_alignments" falsevalue="" display="checkboxes" label="Save memory on large gappy alignments" help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments." optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	393 ## (-V)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	394 <param name="disable_rate_heterogeneity" type="boolean" checked="no" truevalue="--disable_raite_heterogeneity" falsevalue="" display="checkboxes" label="Disable rate heterogeneity" help="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead. Only works if you specify the CAT model of rate heterogeneity." optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	395 ## (-W)
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	396 <param name="sliding_window_size" type="integer" value="" label="Sliding window size" optional="True" help="Sliding window size for leave-one-out site-specific placement bias algorithm. Only effective when used in combination with '-f S'. Default is '100 sites'" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	397 ## (-x) - see it by the (-b)
96915eee708d Uploaded tiagoantao parents: diff changeset	398 ## (-y)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	399 <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="--parsimony_starting_tree_only" falsevalue="" display="checkboxes" label="Compute a randomized parsimony starting tree only" optional="True" help="If you want to only compute a parsimony starting tree with RAxML specify '-y'. The program will exit after computation of the starting tree." />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	400 ## (-z)
20 d930ea30718d planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501 tiagoantao parents: 19 diff changeset	401 <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file" help="Specify the file name of a file containing multiple trees e.g. from a bootstrap that shall be used to draw bipartition values onto a tree provided with '-t', It can also be used to compute per site log likelihoods in combination with '-f g' and to read a bunch of trees for '-f h', '-f m' and '-f n'." optional="True" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	402 </when> ## full option list
96915eee708d Uploaded tiagoantao parents: diff changeset	403 </conditional> ## END $selExtraOpts
96915eee708d Uploaded tiagoantao parents: diff changeset	404 </inputs>
96915eee708d Uploaded tiagoantao parents: diff changeset	405 <outputs>
96915eee708d Uploaded tiagoantao parents: diff changeset	406 <data format="txt" name="info" from_work_dir="RAxML_info.galaxy" label="Info" />
96915eee708d Uploaded tiagoantao parents: diff changeset	407 ## REQUIRED
96915eee708d Uploaded tiagoantao parents: diff changeset	408 <data format="txt" name="logReq" from_work_dir="RAxML_log.galaxy" label="Log">
96915eee708d Uploaded tiagoantao parents: diff changeset	409 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	410 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	411 </data>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	412 <data format="nhx" name="parsimonyTreeReq" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	413 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	414 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	415 </data>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	416 <data format="nhx" name="resultReq" from_work_dir="RAxML_result.galaxy" label="Result">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	417 <filter>(selExtraOpts['extraOptions'] == 'required')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	418 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	419 </data>
96915eee708d Uploaded tiagoantao parents: diff changeset	420 ## ADVANCED
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	421 <data format="nhx" name="randomTree" from_work_dir="RAxML_randomTree.galaxy" label="Random Tree">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	422 <filter>selExtraOpts['search_complete_random_tree'] is True</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	423 <filter>selExtraOpts['extraOptions'] == "full"</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	424 </data>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	425 <data format="nhx" name="bestTree" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
45 c7c3ba18e828 planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 43 diff changeset	426 <!-- <filter>(selExtraOpts['extraOptions'] == 'full')</filter> -->
c7c3ba18e828 planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 43 diff changeset	427 <!-- <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
42 fd919b8a31c6 planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 41 diff changeset	428 <filter>(selExtraOpts['majority_rule_consensus'] == '')</filter> -->
0 96915eee708d Uploaded tiagoantao parents: diff changeset	429 </data>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	430 <data format="nhx" name="bestTreeMultipleModel" from_work_dir="RAxML_bestTree.galaxy" label="Best-scoring ML Tree">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	431 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	432 <filter>(selExtraOpts['multiple_model'] != '')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	433 </data>
96915eee708d Uploaded tiagoantao parents: diff changeset	434 <data format="txt" name="bestTreeMultipleModelPartitions" from_work_dir="RAxML_bestTreePartitions.galaxy" label="Best-scoring ML Tree Partitions">
96915eee708d Uploaded tiagoantao parents: diff changeset	435 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	436 <filter>selExtraOpts['multiple_model'] is not None </filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	437 </data>
96915eee708d Uploaded tiagoantao parents: diff changeset	438 <data format="txt" name="log" from_work_dir="RAxML_log.galaxy" label="Log">
96915eee708d Uploaded tiagoantao parents: diff changeset	439 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	440 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	441 <filter>(selExtraOpts['bootseed'] == '')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	442 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	443 <filter>(selExtraOpts['search_algorithm'] != 'b')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	444 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	445 </data>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	446 <data format="nhx" name="result" from_work_dir="RAxML_result.galaxy" label="Result">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	447 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	448 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	449 <filter>selExtraOpts['bootseed'] == ''</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	450 <filter>selExtraOpts['search_algorithm'] != 'a'</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	451 <filter>selExtraOpts['search_algorithm'] != 'b'</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	452 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	453 </data>
96915eee708d Uploaded tiagoantao parents: diff changeset	454 <data format="txt" name="resultMultipleModelPartitions" from_work_dir="RAxML_resultPartitions.galaxy" label="Result Partitions">
96915eee708d Uploaded tiagoantao parents: diff changeset	455 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	456 <filter>(selExtraOpts['multiple_model'] is not None)</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	457 </data>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	458 <data format="nhx" name="parsimonyTree" from_work_dir="RAxML_parsimonyTree.galaxy" label="Parsimony Tree">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	459 <filter>(selExtraOpts['extraOptions'] == "full")</filter>
55 730aff7a4ae5 planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 54 diff changeset	460 <!--
0 96915eee708d Uploaded tiagoantao parents: diff changeset	461 <filter>(selExtraOpts['rapid_bootstrap_random_seed'] == '')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	462 <filter>(selExtraOpts['bootseed'] == '')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	463 <filter>(selExtraOpts['search_algorithm'] != 'a')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	464 <filter>(selExtraOpts['constraint_file'] is None)</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	465 <filter>(selExtraOpts['groupingfile'] is None)</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	466 <filter>(selExtraOpts['search_complete_random_tree'] is False)</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	467 <filter>(selExtraOpts['start_tree_file'] is None)</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	468 <filter>(selExtraOpts['majority_rule_consensus'] == '') </filter>
55 730aff7a4ae5 planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 54 diff changeset	469 -->
0 96915eee708d Uploaded tiagoantao parents: diff changeset	470 </data>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	471 <data format="nhx" name="bootstrap" from_work_dir="RAxML_bootstrap.galaxy" label="Final Bootstrap Trees">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	472 <filter>selExtraOpts['extraOptions'] == "full"</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	473 <filter>selExtraOpts['number_of_runs'] != '' or selExtraOpts['number_of_runs_bootstop'] != ''</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	474 <filter>selExtraOpts['rapid_bootstrap_random_seed'] != '' or selExtraOpts['bootseed'] != ''</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	475 </data>
96915eee708d Uploaded tiagoantao parents: diff changeset	476 <data format="txt" name="bipartitions" from_work_dir="RAxML_bipartitions.galaxy" label="Bipartitions">
96915eee708d Uploaded tiagoantao parents: diff changeset	477 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	478 <filter>selExtraOpts['extraOptions'] == "full"</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	479 </data>
96915eee708d Uploaded tiagoantao parents: diff changeset	480 <data format="txt" name="bipartitionsBranchLabels" from_work_dir="RAxML_bipartitionsBranchLabels.galaxy" label="Bipartitions Branch Labels">
96915eee708d Uploaded tiagoantao parents: diff changeset	481 <filter>selExtraOpts['extraOptions'] == "full"</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	482 <filter>(selExtraOpts['search_algorithm'] == 'b') or ((selExtraOpts['search_algorithm'] == 'a') and (selExtraOpts['rapid_bootstrap_random_seed'] != '')) </filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	483 </data>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	484 <data format="nhx" name="strictConsensusTree" from_work_dir="RAxML_StrictConsensusTree.galaxy" label="Strict Consensus Tree">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	485 <filter>selExtraOpts['extraOptions'] == "full"</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	486 <filter>(selExtraOpts['majority_rule_consensus'] == 'STRICT') </filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	487 </data>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	488 <data format="nhx" name="majorityRuleConsensusTree" from_work_dir="RAxML_MajorityRuleConsensusTree.galaxy" label="Majority Rule Consensus Tree">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	489 <filter>selExtraOpts['extraOptions'] == "full"</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	490 <filter>(selExtraOpts['majority_rule_consensus'] == 'MR')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	491 </data>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	492 <data format="nhx" name="majorityRuleExtendedConsensusTree" from_work_dir="RAxML_MajorityRuleExtendedConsensusTree.galaxy" label="Majority Rule Extended Consensus Tree">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	493 <filter>selExtraOpts['extraOptions'] == "full"</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	494 <filter>(selExtraOpts['majority_rule_consensus'] == 'MRE')</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	495 </data>
96915eee708d Uploaded tiagoantao parents: diff changeset	496 <data format="txt" name="bipartitionFreq" from_work_dir="RAxML_bipartitionFrequences.galaxy" label="Pair-wise bipartition frequences.">
96915eee708d Uploaded tiagoantao parents: diff changeset	497 <filter>selExtraOpts['search_algorithm'] == 'm' </filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	498 <filter>selExtraOpts['extraOptions'] == "full"</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	499 </data>
96915eee708d Uploaded tiagoantao parents: diff changeset	500 <data format="txt" name="perSiteLLs" from_work_dir="RAxML_perSiteLLs.galaxy" label="Per-site likelihood schores">
96915eee708d Uploaded tiagoantao parents: diff changeset	501 <filter>selExtraOpts['search_algorithm'] == 'g' </filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	502 <filter>selExtraOpts['extraOptions'] == "full"</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	503 </data>
96915eee708d Uploaded tiagoantao parents: diff changeset	504 <data format="txt" name="distances" from_work_dir="RAxML_distances.galaxy" label="Pair-wise distances">
96915eee708d Uploaded tiagoantao parents: diff changeset	505 <filter>selExtraOpts['search_algorithm'] == 'x' </filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	506 <filter>selExtraOpts['extraOptions'] == "full"</filter>
96915eee708d Uploaded tiagoantao parents: diff changeset	507 </data>
96915eee708d Uploaded tiagoantao parents: diff changeset	508 </outputs>
96915eee708d Uploaded tiagoantao parents: diff changeset	509 <tests>
96915eee708d Uploaded tiagoantao parents: diff changeset	510 <test>
96915eee708d Uploaded tiagoantao parents: diff changeset	511 <param name="extraOptions" value="required"/>
7 942aa40bd86c planemo upload commit 3ac7fc026930ed9a7951e0a937c16d2af2f1499a-dirty tiagoantao parents: 6 diff changeset	512 <param name="infile" value="dna.phy"/>
5 b921c26a1cbc planemo upload commit 3ac7fc026930ed9a7951e0a937c16d2af2f1499a-dirty tiagoantao parents: 4 diff changeset	513 <param name="model_type" value="nucleotide"/>
b921c26a1cbc planemo upload commit 3ac7fc026930ed9a7951e0a937c16d2af2f1499a-dirty tiagoantao parents: 4 diff changeset	514 <param name="base_model" value="GTRCAT"/>
53 9fb69dea6b69 planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 52 diff changeset	515 <output name="parsimonyTreeReq" file="RAxML_parsimonyTree.galaxy.basic" />
50 7bfca3137b5b planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 49 diff changeset	516 <output name="bestTree">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	517 <assert_contents>
11 d9849b4a003b planemo upload commit 1937f464a877ed056bb7f228d51448e94f69cb9a tiagoantao parents: 7 diff changeset	518 <has_text_matching expression="Frog" />
0 96915eee708d Uploaded tiagoantao parents: diff changeset	519 </assert_contents>
96915eee708d Uploaded tiagoantao parents: diff changeset	520 </output>
96915eee708d Uploaded tiagoantao parents: diff changeset	521 </test>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	522 <test>
c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	523 <param name="extraOptions" value="full"/>
c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	524 <param name="infile" value="dna.fasta"/>
c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	525 <param name="model_type" value="nucleotide"/>
c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	526 <param name="base_model" value="GTRCAT"/>
c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	527 <param name="number_of_runs" value="5"/>
54 6e672cd847df planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 53 diff changeset	528 <output name="parsimonyTree">
6e672cd847df planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 53 diff changeset	529 <assert_contents>
6e672cd847df planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 53 diff changeset	530 <has_text_matching expression="Chicken" />
6e672cd847df planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 53 diff changeset	531 <has_text_matching expression="RUN.4" />
6e672cd847df planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 53 diff changeset	532 </assert_contents>
6e672cd847df planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 53 diff changeset	533 </output>
50 7bfca3137b5b planemo upload commit 7a61e716e89a49e8cd50e6653e986a0683f20b91-dirty tiagoantao parents: 49 diff changeset	534 <output name="bestTree">
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	535 <assert_contents>
48 aadc64648050 planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 47 diff changeset	536 <has_text_matching expression="Whale" />
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	537 </assert_contents>
c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	538 </output>
c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	539 </test>
0 96915eee708d Uploaded tiagoantao parents: diff changeset	540 </tests>
96915eee708d Uploaded tiagoantao parents: diff changeset	541 <help>
96915eee708d Uploaded tiagoantao parents: diff changeset	542 Title:
96915eee708d Uploaded tiagoantao parents: diff changeset	543 ______
96915eee708d Uploaded tiagoantao parents: diff changeset	544 Randomized Axelerated Maximum Likelihood
96915eee708d Uploaded tiagoantao parents: diff changeset	545
96915eee708d Uploaded tiagoantao parents: diff changeset	546 Description:
96915eee708d Uploaded tiagoantao parents: diff changeset	547 ____________
96915eee708d Uploaded tiagoantao parents: diff changeset	548
96915eee708d Uploaded tiagoantao parents: diff changeset	549 RAxML is a program for Maximum Likelihood-based inference of large phylogenetic
96915eee708d Uploaded tiagoantao parents: diff changeset	550 trees. The program is explicitly being developed to efficiently infer trees for
96915eee708d Uploaded tiagoantao parents: diff changeset	551 extremely large datasets, either in terms of the number of taxa and/or the
96915eee708d Uploaded tiagoantao parents: diff changeset	552 sequence length.
96915eee708d Uploaded tiagoantao parents: diff changeset	553
96915eee708d Uploaded tiagoantao parents: diff changeset	554 URL:
96915eee708d Uploaded tiagoantao parents: diff changeset	555 ____
96915eee708d Uploaded tiagoantao parents: diff changeset	556 Author's page: http://www.exelixis-lab.org/
96915eee708d Uploaded tiagoantao parents: diff changeset	557
96915eee708d Uploaded tiagoantao parents: diff changeset	558 Help: http://groups.google.com/group/raxml
96915eee708d Uploaded tiagoantao parents: diff changeset	559
96915eee708d Uploaded tiagoantao parents: diff changeset	560
96915eee708d Uploaded tiagoantao parents: diff changeset	561 Tool development:
96915eee708d Uploaded tiagoantao parents: diff changeset	562 -----------------
96915eee708d Uploaded tiagoantao parents: diff changeset	563 Oleksandr Moskalenko with adaptations from Tiago Antao.
96915eee708d Uploaded tiagoantao parents: diff changeset	564
96915eee708d Uploaded tiagoantao parents: diff changeset	565 </help>
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	566 <citations>
c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	567 <citation type="doi">10.1093/bioinformatics/btu033</citation>
c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	568 <citation type="bibtex">
0 96915eee708d Uploaded tiagoantao parents: diff changeset	569 @article{stamatakis2014raxml,
96915eee708d Uploaded tiagoantao parents: diff changeset	570 title={RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies},
96915eee708d Uploaded tiagoantao parents: diff changeset	571 author={Stamatakis, Alexandros},
96915eee708d Uploaded tiagoantao parents: diff changeset	572 journal={Bioinformatics},
96915eee708d Uploaded tiagoantao parents: diff changeset	573 volume={30},
96915eee708d Uploaded tiagoantao parents: diff changeset	574 number={9},
96915eee708d Uploaded tiagoantao parents: diff changeset	575 pages={1312--1313},
96915eee708d Uploaded tiagoantao parents: diff changeset	576 year={2014},
96915eee708d Uploaded tiagoantao parents: diff changeset	577 publisher={Oxford Univ Press}}
24 c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	578 </citation>
c9fd05a8751e planemo upload commit 34bbc567766bf5b1986ee91bb3e46c542a45e658-dirty tiagoantao parents: 23 diff changeset	579 </citations>
0 96915eee708d Uploaded tiagoantao parents: diff changeset	580 </tool>

Mercurial > repos > tiagoantao > raxml

annotate raxml.xml @ 55:730aff7a4ae5 draft default tip