Mercurial > repos > greg > plant_tribes_gene_family_phylogeny_builder

comparison macros.xml @ 0:7000422fbaff draft

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author greg
date Thu, 08 Jun 2017 12:51:58 -0400
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-1:000000000000 0:7000422fbaff
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>
6 <requirement type="package" version="1.0.0">plant_tribes_assembly_post_processor</requirement>
7 </requirements>
8 </xml>
9 <xml name="requirements_gene_family_aligner">
10 <requirements>
11 <requirement type="package" version="1.0.0">plant_tribes_gene_family_aligner</requirement>
12 </requirements>
13 </xml>
14 <xml name="requirements_gene_family_classifier">
15 <requirements>
16 <requirement type="package" version="1.0.0">plant_tribes_gene_family_classifier</requirement>
17 </requirements>
18 </xml>
19 <xml name="requirements_gene_family_integrator">
20 <requirements>
21 <requirement type="package" version="1.0.0">plant_tribes_gene_family_integrator</requirement>
22 </requirements>
23 </xml>
24 <xml name="requirements_kaks_analysis">
25 <requirements>
26 <requirement type="package" version="1.0.0">plant_tribes_kaks_analysis</requirement>
27 </requirements>
28 </xml>
29 <xml name="requirements_ks_distribution">
30 <requirements>
31 <requirement type="package" version="1.3.0">r-optparse</requirement>
32 </requirements>
33 </xml>
34 <xml name="requirements_gene_family_phylogeny_builder">
35 <requirements>
36 <requirement type="package" version="1.0.0">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">
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>