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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/phyml commit fd76965826549db42ae414b80e4254089babe6a5
author iuc
date Mon, 23 Oct 2023 17:15:37 +0000
parents 2bf47d57ebb5
children
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2:2bf47d57ebb5 3:7157a5b34a68
1 <tool id="phyml" name="PhyML" version="@VERSION@"> 1 <tool id="phyml" name="PhyML" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
2 <description>Phylogeny software based on the maximum-likelihood method.</description> 2 <description>Phylogeny software based on the maximum-likelihood method</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">3.3.20190909</token> 4 <token name="@TOOL_VERSION@">3.3.20220408</token>
5 <token name="@VERSION_SUFFIX@">0</token>
5 </macros> 6 </macros>
7 <xrefs>
8 <xref type="bio.tools">phyml</xref>
9 </xrefs>
6 <requirements> 10 <requirements>
7 <requirement type="package" version="@VERSION@">phyml</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">phyml</requirement>
8 </requirements> 12 </requirements>
13 <stdio>
14 <regex source="stdout" match="failed" level="fatal" description="PhyML failed"/>
15 </stdio>
9 <version_command> 16 <version_command>
10 <![CDATA[ phyml --version ]]> 17 <![CDATA[ phyml --version || true ]]>
11 </version_command> 18 </version_command>
12 <command detect_errors="default"> 19 <command>
13 <![CDATA[ 20 <![CDATA[
21 #import re
14 ##PhyML outputs are based on input path and we need to create outputs in working_dir. 22 ##PhyML outputs are based on input path and we need to create outputs in working_dir.
15 ln -sf '$input' '${input.name}' && 23 #set input_name = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
16 #if $userInputTree: 24 ln -sf '$input' '$input_name' &&
17 ln -sf '${$userInputTree}' '${$userInputTree.name}' && 25 #if $userInputTree
26 #set userInputTree_name = re.sub('[^\s\w\-]', '_', str($userInputTree_name.element_identifier))
27 ln -sf '$$userInputTree' '$userInputTree_name' &&
18 #end if 28 #end if
19 29
20 phyml --input '${input.name}' 30 phyml --input '$input_name'
21 '${phylip_format}' 31 ${phylip_format}
22 --datatype '${seq.type_of_seq}' 32 --datatype '${seq.type_of_seq}'
23 --multiple '${nb_data_set}' 33 --multiple '${nb_data_set}'
24 34
25 #if (str($support_condition.branchSupport) in ['0','-1','-2','-4','-5']): 35 #if (str($support_condition.branchSupport) in ['0','-1','-2','-4','-5']):
26 --bootstrap '${support_condition.branchSupport}' 36 --bootstrap '${support_condition.branchSupport}'
27 #else: 37 #else:
28 --bootstrap '${support_condition.branchSupport.replicate}' 38 --bootstrap '${support_condition.replicate}'
29 #end if 39 #end if
30 40
41 --model '${seq.model}'
31 #if $seq.type_of_seq == "nt": 42 #if $seq.type_of_seq == "nt":
32 -t '${seq.tstv}' 43 -t '${seq.tstv}'
33 #end if 44 #end if
34 45
35 --model '${seq.model}'
36 -f '${equi_freq}' 46 -f '${equi_freq}'
37 --pinv '${prop_invar}' 47 --pinv '${prop_invar}'
38 48
39 --nclasses '${nbSubstCat}' 49 --nclasses '${nbSubstCat}'
40 50
44 54
45 --search '${move}' 55 --search '${move}'
46 -o '${optimisationTopology}' 56 -o '${optimisationTopology}'
47 57
48 #if $userInputTree: 58 #if $userInputTree:
49 --inputtree '${$userInputTree.name}' 59 --inputtree '${$userInputTree_name}'
50 #end if 60 #end if
51 61
52 #if $numStartSeed != "0": 62 #if $numStartSeed != "0":
53 --r_seed '${numStartSeed}' 63 --r_seed '${numStartSeed}'
54 #end if 64 #end if
55 65
56 --no_memory_check > '${output_stdout}' && 66 --no_memory_check
57 grep 'failed' '${output_stdout}' >&2; 67 | tee '${output_stdout}'
58 ]]> 68 ]]>
59 </command> 69 </command>
60 <inputs> 70 <inputs>
61 <param name="input" type="data" format="phylip,phy" label="Alignment file" help="phylip format"/> 71 <param argument="--input" type="data" format="phylip,phy" label="Alignment file" help="phylip format"/>
62 <param name="phylip_format" type="select" label="Changes interleaved format"> 72 <param argument="--sequential" name="phylip_format" type="select" label="Changes interleaved format">
63 <option value="">Interleaved</option> 73 <option value="">Interleaved</option>
64 <option value="--sequential">Sequential</option> 74 <option value="--sequential">Sequential</option>
65 </param> 75 </param>
66 <param name="nb_data_set" type="integer" min="1" value="1" label="Number of data sets" /> 76 <param argument="--multiple" name="nb_data_set" type="integer" min="1" value="1" label="Number of data sets" />
67 <conditional name="seq"> 77 <conditional name="seq">
68 <param name="type_of_seq" type="select" label="Data type"> 78 <param argument="--datatype name" name="type_of_seq" type="select" label="Data type">
69 <option value="nt">Nucleic acids</option> 79 <option value="nt">Nucleic acids</option>
70 <option value="aa">Amino acids</option> 80 <option value="aa">Amino acids</option>
71 </param> 81 </param>
72 <when value="nt"> 82 <when value="nt">
73 <param name="tstv" type="text" value="e" label="Transition/transversion ratio" help="Must be a positive integer, 'e' if you want PhyML to estimate it" /> 83 <param argument="--ts/tv" name="tstv" type="text" value="e" label="Transition/transversion ratio" help="Must be a positive integer, 'e' if you want PhyML to estimate it" />
74 <param name="model" type="select" label="Substitution model"> 84 <param argument="--model" type="select" label="Substitution model">
75 <option value="HKY85">HKY85</option> 85 <option value="HKY85">HKY85</option>
76 <option value="JC69">JC69</option> 86 <option value="JC69">JC69</option>
77 <option value="K80">K80</option> 87 <option value="K80">K80</option>
78 <option value="F81">F81</option> 88 <option value="F81">F81</option>
79 <option value="F84">F84</option> 89 <option value="F84">F84</option>
80 <option value="TN93">TN93</option> 90 <option value="TN93">TN93</option>
81 <option value="GTR">GTR</option> 91 <option value="GTR">GTR</option>
82 </param> 92 </param>
83 </when> 93 </when>
84 <when value="aa"> 94 <when value="aa">
85 <param name="model" type="select" label="Evolution model"> 95 <param argument="--model" type="select" label="Evolution model">
86 <option value="LG">LG</option> 96 <option value="LG">LG</option>
87 <option value="WAG">WAG</option> 97 <option value="WAG">WAG</option>
88 <option value="JTT">JTT</option> 98 <option value="JTT">JTT</option>
89 <option value="MtREV">MtREV</option> 99 <option value="MtREV">MtREV</option>
90 <option value="Dayhoff">Dayhoff</option> 100 <option value="Dayhoff">Dayhoff</option>
98 <option value="HIVw">HIVw</option> 108 <option value="HIVw">HIVw</option>
99 <option value="HIVb">HIVb</option> 109 <option value="HIVb">HIVb</option>
100 </param> 110 </param>
101 </when> 111 </when>
102 </conditional> 112 </conditional>
103 <param name="prop_invar" type="text" value="e" label="Proportion of invariant sites" help="Can be a fixed value in the [0,1] range or 'e' to get the maximum likelihood estimate, 0 to ignore this parameter"/> 113 <param argument="--pinvname" name="prop_invar" type="text" value="e" label="Proportion of invariant sites" help="Can be a fixed value in the [0,1] range or 'e' to get the maximum likelihood estimate, 0 to ignore this parameter"/>
104 <param name="equi_freq" type="select" label="Equilibrium frequencies" help="Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model: frequencies are estimated using ML for nucleotides or defined by the proteic substitution model."> 114 <param argument="-f" name="equi_freq" type="select" label="Equilibrium frequencies" help="Empirical: frequencies are estimated by counting the occurences in the alignment. ML/Model: frequencies are estimated using ML for nucleotides or defined by the proteic substitution model.">
105 <option value="m">ML/Model</option> 115 <option value="m">ML/Model</option>
106 <option value="e">Empirical</option> 116 <option value="e">Empirical</option>
107 </param> 117 </param>
108 <param name="nbSubstCat" type="integer" min="1" value="4" label="Number of categories for the discrete gamma model" help="1 means no gamma model" /> 118 <param argument="--nclasses" name="nbSubstCat" type="integer" min="1" value="4" label="Number of categories for the discrete gamma model" help="1 means no gamma model" />
109 <param name="gamma" type="text" value="e" label="Parameter of the gamma model" help="'e' if you want PhyML to estimate it"/> 119 <param argument="--alpha" name="gamma" type="text" value="e" label="Parameter of the gamma model" help="'e' if you want PhyML to estimate it"/>
110 <param name="move" type="select" label="Tree topology search"> 120 <param argument="--search" name="move" type="select" label="Tree topology search">
111 <option value="NNI">NNI (Nearest Neighbor Interchange)</option> 121 <option value="NNI">NNI (Nearest Neighbor Interchange)</option>
112 <option value="SPR">SPR (Subtree Pruning and Regraphing)</option> 122 <option value="SPR">SPR (Subtree Pruning and Regraphing)</option>
113 <option value="BEST">Best of NNI and SPR</option> 123 <option value="BEST">Best of NNI and SPR</option>
114 </param> 124 </param>
115 <param name="optimisationTopology" type="select" label="Optimise topology"> 125 <param argument="-o" name="optimisationTopology" type="select" label="Optimise topology">
116 <option value="tlr">Tree topology, Branch length, Rate parameter</option> 126 <option value="tlr">Tree topology, Branch length, Rate parameter</option>
117 <option value="tl">Tree topology, Branch length</option> 127 <option value="tl">Tree topology, Branch length</option>
118 <option value="l">Branch length</option> 128 <option value="l">Branch length</option>
119 <option value="r">Rate parameter</option> 129 <option value="r">Rate parameter</option>
120 <option value="n">No parameter is optimized</option> 130 <option value="n">No parameter is optimized</option>
121 </param> 131 </param>
122 <conditional name="support_condition"> 132 <conditional name="support_condition">
123 <param name="branchSupport" type="select" label="Statistical tests for branch support" help="Use aLRT or aBayes to save computing time"> 133 <param argument="--bootstrap" name="branchSupport" type="select" label="Statistical tests for branch support" help="Use aLRT or aBayes to save computing time">
124 <option value="0">No bootstrap</option> 134 <option value="0">No bootstrap</option>
125 <option value="1">Bootstrap</option> 135 <option value="1">Bootstrap</option>
126 <option value="-1">likelihood aLRT statistics</option> 136 <option value="-1">likelihood aLRT statistics</option>
127 <option value="-2">likelihood Chi2-based</option> 137 <option value="-2">likelihood Chi2-based</option>
128 <option value="-4" selected='true'>SH-like</option> 138 <option value="-4" selected='true'>SH-like</option>
129 <option value="-5">Approximate Bayes branch supports</option> 139 <option value="-5">Approximate Bayes branch supports</option>
130 </param> 140 </param>
131 <when value="0"/> 141 <when value="0"/>
132 <when value="-1"/> 142 <when value="-1"/>
133 <when value="-2"/> 143 <when value="-2"/>
134 <when value="-4"/> 144 <when value="-4"/>
135 <when value="-5"/> 145 <when value="-5"/>
136 <when value="1"> 146 <when value="1">
137 <param name="replicate" type="integer" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer" /> 147 <param argument="--bootstrap" name="replicate" type="integer" min="1" value="100" label="Number of bootstrap replicates" help="Must be a positive integer" />
138 </when> 148 </when>
139 </conditional> 149 </conditional>
140 <param name="numStartSeed" type="integer" value="0" label="Number of seed used to initiate the random number generator" help="0 to random seed"/> 150 <param argument="--r_seed" name="numStartSeed" type="integer" value="0" label="Number of seed used to initiate the random number generator" help="0 to random seed"/>
141 <param name="userInputTree" optional="True" type="data" format="nhx" label="Tree file" help="newick format"/> 151 <param argument="--inputtree" name="userInputTree" optional="true" type="data" format="nhx" label="Tree file" help="newick format"/>
142 </inputs> 152 </inputs>
143 <outputs> 153 <outputs>
144 <data name="output_tree" format="nhx" label="PhyML Newick tree: ${input.name}.nwk" from_work_dir="*_phyml_tree.txt" /> 154 <data name="output_tree" format="nhx" label="PhyML Newick tree: ${input.name}.nwk" from_work_dir="*_phyml_tree.txt" />
145 <data name="output_stats" format="txt" label="PhyML Statistic: ${input.name}.stats.txt" from_work_dir="*_phyml_stats.txt"/> 155 <data name="output_stats" format="txt" label="PhyML Statistic: ${input.name}.stats.txt" from_work_dir="*_phyml_stats.txt"/>
146 <data name="output_stdout" format="txt" label="PhyML Stdout: ${input.name}"/> 156 <data name="output_stdout" format="txt" label="PhyML Stdout: ${input.name}"/>