Mercurial > repos > greg > plant_tribes_kaks_analysis
comparison macros.xml @ 3:1fb0f2092177 draft
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author | greg |
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date | Mon, 30 Oct 2017 09:54:20 -0400 |
parents | 2fe7044626ac |
children | 84615d553d44 |
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2:2fe7044626ac | 3:1fb0f2092177 |
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1 <?xml version='1.0' encoding='UTF-8'?> | 1 <?xml version='1.0' encoding='UTF-8'?> |
2 <macros> | 2 <macros> |
3 <token name="@WRAPPER_VERSION@">1.0</token> | 3 <token name="@WRAPPER_VERSION@">1.0</token> |
4 <xml name="requirements_assembly_post_processor"> | |
5 <requirements> | |
6 <requirement type="package" version="1.0.2">plant_tribes_assembly_post_processor</requirement> | |
7 </requirements> | |
8 </xml> | |
9 <xml name="requirements_gene_family_aligner"> | |
10 <requirements> | |
11 <requirement type="package" version="1.0.2">plant_tribes_gene_family_aligner</requirement> | |
12 </requirements> | |
13 </xml> | |
14 <xml name="requirements_gene_family_classifier"> | |
15 <requirements> | |
16 <requirement type="package" version="1.0.2">plant_tribes_gene_family_classifier</requirement> | |
17 </requirements> | |
18 </xml> | |
19 <xml name="requirements_gene_family_integrator"> | |
20 <requirements> | |
21 <requirement type="package" version="1.0.2">plant_tribes_gene_family_integrator</requirement> | |
22 </requirements> | |
23 </xml> | |
24 <xml name="requirements_kaks_analysis"> | |
25 <requirements> | |
26 <requirement type="package" version="1.0.2">plant_tribes_kaks_analysis</requirement> | |
27 </requirements> | |
28 </xml> | |
29 <xml name="requirements_ks_distribution"> | |
30 <requirements> | |
31 <requirement type="package" version="1.3.2">r-optparse</requirement> | |
32 </requirements> | |
33 </xml> | |
34 <xml name="requirements_gene_family_phylogeny_builder"> | |
35 <requirements> | |
36 <requirement type="package" version="1.0.2">plant_tribes_gene_family_phylogeny_builder</requirement> | |
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"> | 4 <xml name="param_method"> |
46 <param name="method" type="select" label="Protein clustering method"> | 5 <param name="method" type="select" label="Protein clustering method"> |
47 <option value="gfam" selected="true">GFam</option> | 6 <option value="gfam" selected="true">GFam</option> |
48 <option value="orthofinder">OrthoFinder</option> | 7 <option value="orthofinder">OrthoFinder</option> |
49 <option value="orthomcl">OrthoMCL</option> | 8 <option value="orthomcl">OrthoMCL</option> |
50 </param> | 9 </param> |
51 </xml> | 10 </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"> | 11 <xml name="param_scaffold"> |
65 <param name="scaffold" type="select" label="Gene family scaffold"> | 12 <param name="scaffold" type="select" label="Gene family scaffold"> |
66 <options from_data_table="plant_tribes_scaffolds" /> | 13 <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." /> | 14 <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> | 15 </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> | 16 </xml> |
120 <xml name="citation1"> | 17 <xml name="citation1"> |
121 <citation type="bibtex"> | 18 <citation type="bibtex"> |
122 @misc{None, | 19 @misc{None, |
123 journal = {None}, | 20 journal = {None}, |