|
46
|
1 <tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.3.0">
|
|
6
|
2 <description>builds phylogenetic trees of aligned orthologous gene family clusters</description>
|
|
0
|
3 <macros>
|
|
|
4 <import>macros.xml</import>
|
|
|
5 </macros>
|
|
51
|
6 <requirements>
|
|
|
7 <requirement type="package" version="1.0.3">plant_tribes_gene_family_phylogeny_builder</requirement>
|
|
|
8 </requirements>
|
|
38
|
9 <command detect_errors="exit_code"><![CDATA[
|
|
46
|
10 #set input_dir = 'input_dir'
|
|
38
|
11 #set tree_inference = $tree_inference_cond.tree_inference
|
|
|
12 #if str($tree_inference) == 'raxml':
|
|
|
13 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
|
|
|
14 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
|
|
|
15 #if str($rooting_order_file) == 'yes':
|
|
|
16 #set rooting_order = $rooting_order_file_cond.rooting_order
|
|
|
17 #end if
|
|
|
18 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
|
|
|
19 #end if
|
|
46
|
20 mkdir $input_dir &&
|
|
47
|
21 #for $i in $input:
|
|
48
|
22 #set filename = $i.file_name
|
|
51
|
23 #set name = $i.name
|
|
50
|
24 ln -s $filename $input_dir/$name &&
|
|
46
|
25 #end for
|
|
43
|
26 GeneFamilyPhylogenyBuilder
|
|
46
|
27 --orthogroup_aln '$input_dir'
|
|
38
|
28 --scaffold '$scaffold.fields.path'
|
|
|
29 --config_dir '$scaffold.fields.path'
|
|
|
30 --method $method
|
|
|
31 --tree_inference $tree_inference
|
|
|
32 #if str($tree_inference) == 'raxml':
|
|
|
33 #if str($rooting_order_file) == 'yes':
|
|
|
34 --rooting_order '$rooting_order'
|
|
|
35 ## No else block needed here because the default rooting_order
|
|
|
36 ## configuration will be used if the --rooting_order flag is missing.
|
|
|
37 #end if
|
|
|
38 --bootstrap_replicates $bootstrap_replicates
|
|
|
39 #end if
|
|
|
40 --min_orthogroup_size $min_orthogroup_size
|
|
|
41 --max_orthogroup_size $max_orthogroup_size
|
|
|
42 --num_threads \${GALAXY_SLOTS:-4}
|
|
|
43 ]]></command>
|
|
0
|
44 <inputs>
|
|
46
|
45 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup alignments" />
|
|
0
|
46 <expand macro="param_scaffold" />
|
|
|
47 <expand macro="param_method" />
|
|
|
48 <conditional name="tree_inference_cond">
|
|
6
|
49 <param name="tree_inference" type="select" label="Phylogenetic inference method">
|
|
0
|
50 <option value="raxml" selected="true">RAxML</option>
|
|
|
51 <option value="fasttree">FastTree</option>
|
|
|
52 </param>
|
|
|
53 <when value="raxml">
|
|
|
54 <conditional name="rooting_order_file_cond">
|
|
7
|
55 <param name="rooting_order_file" type="select" label="Rooting order configuration">
|
|
0
|
56 <option value="no" selected="true">No</option>
|
|
|
57 <option value="yes">Yes</option>
|
|
|
58 </param>
|
|
|
59 <when value="no" />
|
|
|
60 <when value="yes">
|
|
11
|
61 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration" />
|
|
0
|
62 </when>
|
|
|
63 </conditional>
|
|
6
|
64 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Bootstrap replicates" />
|
|
0
|
65 </when>
|
|
|
66 <when value="fasttree" />
|
|
|
67 </conditional>
|
|
27
|
68 <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" />
|
|
|
69 <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" />
|
|
0
|
70 </inputs>
|
|
|
71 <outputs>
|
|
43
|
72 <collection name="tree" type="list" label="${tool.name} (phylogenetic trees) on ${on_string}">
|
|
29
|
73 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" />
|
|
|
74 </collection>
|
|
43
|
75 <collection name="phylip" type="list" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}">
|
|
25
|
76 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
|
|
43
|
77 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" />
|
|
|
78 </collection>
|
|
0
|
79 </outputs>
|
|
|
80 <tests>
|
|
|
81 <test>
|
|
|
82 </test>
|
|
|
83 </tests>
|
|
|
84 <help>
|
|
6
|
85 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
|
|
|
86 analyses of genome-scale gene families and transcriptomes. This tool performs gene family phylogenetic inference of
|
|
|
87 multiple sequence alignments produced by the GeneFamilyAligner tool.
|
|
0
|
88
|
|
|
89 -----
|
|
|
90
|
|
|
91 **Required options**
|
|
|
92
|
|
6
|
93 * **Orthogroup alignments** - orthogroup alignment fasta files produced by the GeneFamilyAligner tool selected from your history. Depending on how the GeneFamilyAligner tool was executed, these could either be pre-processed alignments, trimmed alignments or both trimmed and filtered alignments.
|
|
|
94 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Download Data Manager tool.
|
|
11
|
95 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
|
|
6
|
96 * **Phylogenetic inference method** - method for estimating orthogroup maximum likelihood (ML) phylogenetic trees. PlantTribes estimates ML phylogenetic trees using either RAxML or FastTree algorithms.
|
|
|
97
|
|
0
|
98 **Other options**
|
|
|
99
|
|
7
|
100 * **Rooting order configuration** - select 'Yes' to enable selection of a rooting order configuration file for RAxML. Scaffold configuration templates (.rootingOrder.config) of how to customize the RAxML ML tree rooting order can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and is also available at the PlantTribes GitHub `repository`_. Phylogenetic tree rooting order settings shown in these templates are used as defaults if 'No' is selected.
|
|
6
|
101 * **Bootstrap replicates** - number of bootstrap replicates for RAxML to conduct a rapid bootstrap analysis and search for the best-scoring ML tree (default = 100).
|
|
11
|
102 * **Maximum orthogroup size** - maximum number of sequences allowed in orthogroup alignments (default = 100).
|
|
|
103 * **Minimum orthogroup size** - minimum number of sequences allowed in orthogroup alignments (default = 4).
|
|
36
|
104 * **Output additional directory of phylogenetic tree files** - selecting 'Yes' will produce an additional output that has an associated directory of files that are copies of the elements of the phylogenetic trees output dataset collection (this output will be used for future downstream tools).
|
|
6
|
105
|
|
9
|
106 .. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config
|
|
|
107
|
|
0
|
108 </help>
|
|
|
109 <citations>
|
|
|
110 <expand macro="citation1" />
|
|
6
|
111 <citation type="bibtex">
|
|
|
112 @article{Wall2008,
|
|
|
113 journal = {Nucleic Acids Research},
|
|
|
114 author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
|
|
|
115 title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
|
|
|
116 year = {2008},
|
|
|
117 volume = {36},
|
|
|
118 number = {suppl 1},
|
|
|
119 pages = {D970-D976},}
|
|
|
120 </citation>
|
|
|
121 <citation type="bibtex">
|
|
|
122 @article{Sasidharan2012,
|
|
|
123 journal = {Nucleic Acids Research},
|
|
|
124 author = {3. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
|
|
|
125 title = {GFam: a platform for automatic annotation of gene families},
|
|
|
126 year = {2012},
|
|
|
127 pages = {gks631},}
|
|
|
128 </citation>
|
|
|
129 <citation type="bibtex">
|
|
|
130 @article{Li2003,
|
|
|
131 journal = {Genome Research}
|
|
|
132 author = {4. Li L, Stoeckert CJ, Roos DS},
|
|
|
133 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
|
|
|
134 year = {2003},
|
|
|
135 volume = {13},
|
|
|
136 number = {9},
|
|
|
137 pages = {2178-2189},}
|
|
|
138 </citation>
|
|
|
139 <citation type="bibtex">
|
|
|
140 @article{Emms2015,
|
|
|
141 journal = {Genome Biology}
|
|
|
142 author = {5. Emms DM, Kelly S},
|
|
|
143 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
|
|
|
144 year = {2015},
|
|
|
145 volume = {16},
|
|
|
146 number = {1},
|
|
|
147 pages = {157},}
|
|
|
148 </citation>
|
|
|
149 <citation type="bibtex">
|
|
|
150 @article{Stamatakis2014,
|
|
|
151 journal = {Bioinformatics},
|
|
|
152 author = {6. Stamatakis A},
|
|
|
153 title = {RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies},
|
|
|
154 year = {2014},
|
|
|
155 url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html},}
|
|
|
156 </citation>
|
|
|
157 <citation type="bibtex">
|
|
|
158 @article{Price2010,
|
|
|
159 journal = {PLoS one},
|
|
|
160 author = {7. Price MN, Dehal PS, Arkin AP},
|
|
|
161 title = {FastTree 2-approximately maximim-likelihood trees for large alignments},
|
|
|
162 year = {2010},
|
|
|
163 volume = {5},
|
|
|
164 number = {3},
|
|
|
165 pages = {e9490},}
|
|
|
166 </citation>
|
|
40
|
167 <citation type="bibtex">
|
|
|
168 @article{Nascimento2016,
|
|
|
169 journal = {Bioinformatics},
|
|
|
170 author = {8. Nascimento M, Sousa A, Ramirez M, Francisco AP, Carriço JA, Vaz C},
|
|
|
171 title = {PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods},
|
|
|
172 year = {2016},
|
|
|
173 volume = {33},
|
|
|
174 number = {1},
|
|
|
175 pages = {128-129},}
|
|
|
176 </citation>
|
|
0
|
177 </citations>
|
|
|
178 </tool>
|
