|
72
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <macros>
|
|
|
3 <xml name="requirements">
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement>
|
|
|
6 </requirements>
|
|
|
7 </xml>
|
|
|
8 <xml name="stdio">
|
|
|
9 <stdio>
|
|
|
10 <exit_code range="1:"/>
|
|
|
11 <exit_code range=":-1"/>
|
|
|
12 <regex match="Error:"/>
|
|
|
13 <regex match="Exception:"/>
|
|
|
14 </stdio>
|
|
|
15 </xml>
|
|
|
16 <xml name="param_scaffold">
|
|
|
17 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
|
|
|
18 <options from_data_table="plant_tribes_scaffolds" />
|
|
|
19 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
|
|
|
20 </param>
|
|
|
21 </xml>
|
|
|
22 <xml name="param_method">
|
|
|
23 <param name="method" type="select" label="Protein clustering method">
|
|
|
24 <option value="gfam" selected="true">GFam</option>
|
|
|
25 <option value="orthofinder">OrthoFinder</option>
|
|
|
26 <option value="orthomcl">OrthoMCL</option>
|
|
|
27 </param>
|
|
|
28 </xml>
|
|
|
29 <xml name="param_options_type">
|
|
|
30 <param name="options_type" type="select" label="Options Configuration">
|
|
|
31 <option value="basic" selected="true">Basic</option>
|
|
|
32 <option value="advanced">Advanced</option>
|
|
|
33 </param>
|
|
|
34 </xml>
|
|
83
|
35 <xml name="cond_orthogroup_fna">
|
|
|
36 <conditional name="orthogroup_fna_cond">
|
|
|
37 <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?">
|
|
|
38 <option value="yes" selected="true">Yes</option>
|
|
|
39 <option value="no">No</option>
|
|
|
40 </param>
|
|
|
41 <when value="yes">
|
|
|
42 <conditional name="options_type_cond">
|
|
85
|
43 <expand macro="param_options_type" />
|
|
83
|
44 <when value="basic" />
|
|
|
45 <when value="advanced">
|
|
88
|
46 <expand macro="cond_remove_gappy_sequences" />
|
|
83
|
47 <expand macro="cond_phylogenetic_trees_ptorthocs" />
|
|
|
48 <expand macro="param_multiple_codon_alignments" />
|
|
|
49 </when>
|
|
|
50 </conditional>
|
|
|
51 </when>
|
|
|
52 <when value="no">
|
|
|
53 <conditional name="options_type_cond">
|
|
86
|
54 <expand macro="param_options_type" />
|
|
83
|
55 <when value="basic" />
|
|
|
56 <when value="advanced">
|
|
88
|
57 <expand macro="cond_remove_gappy_sequences" />
|
|
83
|
58 <expand macro="cond_phylogenetic_trees_ptorthocs" />
|
|
|
59 </when>
|
|
|
60 </conditional>
|
|
|
61 </when>
|
|
|
62 </conditional>
|
|
81
|
63 </xml>
|
|
72
|
64 <xml name="cond_multiple_sequence_alignments">
|
|
|
65 <conditional name="multiple_sequence_alignments_cond">
|
|
|
66 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
|
|
|
67 <option value="no" selected="true">No</option>
|
|
|
68 <option value="yes">Yes</option>
|
|
|
69 </param>
|
|
|
70 <when value="no" />
|
|
|
71 <when value="yes">
|
|
|
72 <conditional name="multiple_sequence_alignments_option_cond">
|
|
|
73 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
|
|
|
74 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
|
|
|
75 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
|
|
|
76 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
|
|
|
77 </param>
|
|
|
78 <when value="create_alignments" />
|
|
|
79 <when value="add_alignments" />
|
|
|
80 <when value="pasta_alignments">
|
|
|
81 <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iterations that the PASTA algorithm will execute" />
|
|
|
82 </when>
|
|
|
83 </conditional>
|
|
|
84 </when>
|
|
|
85 </conditional>
|
|
|
86 </xml>
|
|
79
|
87 <xml name="cond_phylogenetic_trees_ptortho">
|
|
72
|
88 <conditional name="phylogenetic_trees_cond">
|
|
|
89 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
|
|
|
90 <option value="no" selected="true">No</option>
|
|
|
91 <option value="yes">Yes</option>
|
|
|
92 </param>
|
|
|
93 <when value="no" />
|
|
|
94 <when value="yes">
|
|
|
95 <conditional name="tree_inference_cond">
|
|
|
96 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
|
|
|
97 <option value="raxml" selected="true">RAxML</option>
|
|
|
98 <option value="fasttree">FastTree</option>
|
|
|
99 </param>
|
|
|
100 <when value="raxml">
|
|
|
101 <conditional name="rooting_order_file_cond">
|
|
|
102 <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
|
|
|
103 <option value="no" selected="true">No</option>
|
|
|
104 <option value="yes">Yes</option>
|
|
|
105 </param>
|
|
|
106 <when value="no" />
|
|
|
107 <when value="yes">
|
|
|
108 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
|
|
|
109 </when>
|
|
|
110 </conditional>
|
|
|
111 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
|
|
|
112 </when>
|
|
|
113 <when value="fasttree" />
|
|
|
114 </conditional>
|
|
|
115 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
|
|
|
116 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
|
|
75
|
117 </when>
|
|
|
118 </conditional>
|
|
74
|
119 </xml>
|
|
79
|
120 <xml name="cond_phylogenetic_trees_ptorthocs">
|
|
75
|
121 <conditional name="phylogenetic_trees_cond">
|
|
|
122 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
|
|
|
123 <option value="no" selected="true">No</option>
|
|
|
124 <option value="yes">Yes</option>
|
|
|
125 </param>
|
|
|
126 <when value="no" />
|
|
|
127 <when value="yes">
|
|
|
128 <conditional name="tree_inference_cond">
|
|
|
129 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
|
|
|
130 <option value="raxml" selected="true">RAxML</option>
|
|
|
131 <option value="fasttree">FastTree</option>
|
|
|
132 </param>
|
|
|
133 <when value="raxml">
|
|
|
134 <conditional name="rooting_order_file_cond">
|
|
|
135 <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
|
|
|
136 <option value="no" selected="true">No</option>
|
|
|
137 <option value="yes">Yes</option>
|
|
|
138 </param>
|
|
|
139 <when value="no" />
|
|
|
140 <when value="yes">
|
|
|
141 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
|
|
|
142 </when>
|
|
|
143 </conditional>
|
|
|
144 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
|
|
|
145 </when>
|
|
|
146 <when value="fasttree" />
|
|
|
147 </conditional>
|
|
|
148 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
|
|
|
149 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
|
|
|
150 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
|
|
|
151 <option value="protein" selected="true">Amino acid based</option>
|
|
|
152 <option value="dna">Nucleotide based</option>
|
|
|
153 </param>
|
|
72
|
154 </when>
|
|
|
155 </conditional>
|
|
|
156 </xml>
|
|
|
157 <xml name="cond_remove_gappy_sequences">
|
|
|
158 <conditional name="remove_gappy_sequences_cond">
|
|
|
159 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
|
|
|
160 <option value="no" selected="true">No</option>
|
|
|
161 <option value="yes">Yes</option>
|
|
|
162 </param>
|
|
88
|
163 <when value="no">
|
|
|
164 <expand macro="cond_multiple_sequence_alignments" />
|
|
|
165 </when>
|
|
72
|
166 <when value="yes">
|
|
|
167 <conditional name="trim_type_cond">
|
|
|
168 <param name="trim_type" type="select" label="Select process used for gap trimming">
|
|
|
169 <option value="gap_trimming" selected="true">Nucleotide based </option>
|
|
|
170 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
|
|
|
171 </param>
|
|
|
172 <when value="automated_trimming" />
|
|
|
173 <when value="gap_trimming">
|
|
|
174 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps" />
|
|
|
175 </when>
|
|
|
176 </conditional>
|
|
|
177 <conditional name="remove_sequences_with_gaps_cond">
|
|
|
178 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
|
|
|
179 <option value="no" selected="true">No</option>
|
|
|
180 <option value="yes">Yes</option>
|
|
|
181 </param>
|
|
|
182 <when value="no" />
|
|
|
183 <when value="yes">
|
|
|
184 <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" />
|
|
|
185 <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/>
|
|
88
|
186 <expand macro="cond_multiple_sequence_alignments" />
|
|
72
|
187 </when>
|
|
|
188 </conditional>
|
|
|
189 </when>
|
|
|
190 </conditional>
|
|
|
191 </xml>
|
|
74
|
192 <xml name="param_multiple_codon_alignments">
|
|
|
193 <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
|
|
|
194 <option value="no" selected="True">No</option>
|
|
|
195 <option value="yes">Yes</option>
|
|
|
196 </param>
|
|
72
|
197 </xml>
|
|
|
198 <xml name="citations">
|
|
|
199 <citations>
|
|
|
200 <citation type="bibtex">
|
|
|
201 @misc{None,
|
|
|
202 journal = {None},
|
|
|
203 author = {1. Wafula EK},
|
|
|
204 title = {Manuscript in preparation},
|
|
|
205 year = {None},
|
|
|
206 url = {https://github.com/dePamphilis/PlantTribes},}
|
|
|
207 </citation>
|
|
|
208 <citation type="bibtex">
|
|
|
209 @article{Mirarab2014,
|
|
|
210 journal = {Research in Computational Molecular Biology (RECOMB)},
|
|
|
211 author = {2. Mirarab S, Nguyen N, Warnow T},
|
|
|
212 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
|
|
|
213 year = {2014},
|
|
|
214 pages = {177–191},
|
|
|
215 url = {https://github.com/smirarab/pasta},}
|
|
|
216 </citation>
|
|
|
217 <citation type="bibtex">
|
|
|
218 @article{Salvador2009,
|
|
|
219 journal = {Bioinformatics},
|
|
|
220 author = {3. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T},
|
|
|
221 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
|
|
|
222 year = {2009},
|
|
|
223 url = {http://trimal.cgenomics.org},}
|
|
|
224 </citation>
|
|
|
225 <citation type="bibtex">
|
|
|
226 @article{Stamatakis2014,
|
|
|
227 journal = {Bioinformatics},
|
|
|
228 author = {4. Stamatakis A},
|
|
|
229 title = {RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies},
|
|
|
230 year = {2014},
|
|
|
231 url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html},}
|
|
|
232 </citation>
|
|
|
233 <citation type="doi">10.1371/journal.pone.0009490</citation>
|
|
|
234 <citation type="doi">10.1093/bioinformatics/btw412</citation>
|
|
|
235 </citations>
|
|
|
236 </xml>
|
|
|
237 </macros>
|
