|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <macros>
|
|
|
3 <token name="@WRAPPER_VERSION@">1.0</token>
|
|
|
4 <xml name="requirements_assembly_post_processor">
|
|
|
5 <requirements>
|
|
4
|
6 <requirement type="package" version="1.0.2">plant_tribes_assembly_post_processor</requirement>
|
|
0
|
7 </requirements>
|
|
|
8 </xml>
|
|
|
9 <xml name="requirements_gene_family_aligner">
|
|
|
10 <requirements>
|
|
4
|
11 <requirement type="package" version="1.0.2">plant_tribes_gene_family_aligner</requirement>
|
|
0
|
12 </requirements>
|
|
|
13 </xml>
|
|
|
14 <xml name="requirements_gene_family_classifier">
|
|
|
15 <requirements>
|
|
4
|
16 <requirement type="package" version="1.0.2">plant_tribes_gene_family_classifier</requirement>
|
|
0
|
17 </requirements>
|
|
|
18 </xml>
|
|
|
19 <xml name="requirements_gene_family_integrator">
|
|
|
20 <requirements>
|
|
4
|
21 <requirement type="package" version="1.0.2">plant_tribes_gene_family_integrator</requirement>
|
|
0
|
22 </requirements>
|
|
|
23 </xml>
|
|
|
24 <xml name="requirements_kaks_analysis">
|
|
|
25 <requirements>
|
|
4
|
26 <requirement type="package" version="1.0.2">plant_tribes_kaks_analysis</requirement>
|
|
0
|
27 </requirements>
|
|
|
28 </xml>
|
|
|
29 <xml name="requirements_ks_distribution">
|
|
|
30 <requirements>
|
|
4
|
31 <requirement type="package" version="1.3.2">r-optparse</requirement>
|
|
0
|
32 </requirements>
|
|
|
33 </xml>
|
|
|
34 <xml name="requirements_gene_family_phylogeny_builder">
|
|
|
35 <requirements>
|
|
4
|
36 <requirement type="package" version="1.0.2">plant_tribes_gene_family_phylogeny_builder</requirement>
|
|
0
|
37 </requirements>
|
|
|
38 </xml>
|
|
|
39 <xml name="param_codon_alignments">
|
|
|
40 <param name="codon_alignments" type="select" label="Codon alignments">
|
|
|
41 <option value="yes" selected="true">Yes</option>
|
|
|
42 <option value="no">No</option>
|
|
|
43 </param>
|
|
|
44 </xml>
|
|
|
45 <xml name="param_method">
|
|
|
46 <param name="method" type="select" label="Protein clustering method">
|
|
|
47 <option value="gfam" selected="true">GFam</option>
|
|
|
48 <option value="orthofinder">OrthoFinder</option>
|
|
|
49 <option value="orthomcl">OrthoMCL</option>
|
|
|
50 </param>
|
|
|
51 </xml>
|
|
|
52 <xml name="param_options_type">
|
|
|
53 <param name="options_type" type="select" label="Options Configuration">
|
|
|
54 <option value="basic" selected="true">Basic</option>
|
|
|
55 <option value="advanced">Advanced</option>
|
|
|
56 </param>
|
|
|
57 </xml>
|
|
|
58 <xml name="param_orthogroup_fna">
|
|
|
59 <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences">
|
|
|
60 <option value="yes" selected="true">Yes</option>
|
|
|
61 <option value="no">No</option>
|
|
|
62 </param>
|
|
|
63 </xml>
|
|
|
64 <xml name="param_scaffold">
|
|
|
65 <param name="scaffold" type="select" label="Gene family scaffold">
|
|
|
66 <options from_data_table="plant_tribes_scaffolds" />
|
|
|
67 <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." />
|
|
|
68 </param>
|
|
|
69 </xml>
|
|
|
70 <xml name="param_sequence_type">
|
|
|
71 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
|
|
|
72 <option value="protein" selected="true">Amino acid based</option>
|
|
|
73 <option value="dna">Nucleotide based</option>
|
|
|
74 </param>
|
|
|
75 </xml>
|
|
|
76 <xml name="cond_alignment_method">
|
|
|
77 <conditional name="alignment_method_cond">
|
|
|
78 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
|
|
|
79 <option value="mafft" selected="true">MAFFT</option>
|
|
|
80 <option value="pasta">PASTA</option>
|
|
|
81 </param>
|
|
|
82 <when value="mafft" />
|
|
|
83 <when value="pasta">
|
|
|
84 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
|
|
|
85 </when>
|
|
|
86 </conditional>
|
|
|
87 </xml>
|
|
|
88 <xml name="cond_remove_gappy_sequences">
|
|
|
89 <conditional name="remove_gappy_sequences_cond">
|
|
|
90 <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
|
|
|
91 <option value="no" selected="true">No</option>
|
|
|
92 <option value="yes">Yes</option>
|
|
|
93 </param>
|
|
|
94 <when value="no" />
|
|
|
95 <when value="yes">
|
|
|
96 <conditional name="trim_type_cond">
|
|
|
97 <param name="trim_type" type="select" label="Trimming method">
|
|
|
98 <option value="gap_trimming" selected="true">Gap score based trimming</option>
|
|
|
99 <option value="automated_trimming">Automated heuristic trimming</option>
|
|
|
100 </param>
|
|
|
101 <when value="gap_trimming">
|
|
|
102 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
|
|
|
103 </when>
|
|
|
104 <when value="automated_trimming" />
|
|
|
105 </conditional>
|
|
|
106 <conditional name="remove_sequences_with_gaps_cond">
|
|
|
107 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences">
|
|
|
108 <option value="no" selected="true">No</option>
|
|
|
109 <option value="yes">Yes</option>
|
|
|
110 </param>
|
|
|
111 <when value="no" />
|
|
|
112 <when value="yes">
|
|
|
113 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
|
|
|
114 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
|
|
|
115 </when>
|
|
|
116 </conditional>
|
|
|
117 </when>
|
|
|
118 </conditional>
|
|
|
119 </xml>
|
|
|
120 <xml name="citation1">
|
|
|
121 <citation type="bibtex">
|
|
|
122 @misc{None,
|
|
|
123 journal = {None},
|
|
|
124 author = {1. Wafula EK},
|
|
|
125 title = {Manuscript in preparation},
|
|
|
126 year = {None},
|
|
|
127 url = {https://github.com/dePamphilis/PlantTribes},}
|
|
|
128 </citation>
|
|
|
129 </xml>
|
|
|
130 </macros>
|
