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comparison macros.xml @ 0:5ace8af6edb6 draft

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author greg
date Mon, 01 May 2017 13:47:20 -0400
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-1:000000000000 0:5ace8af6edb6
1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros>
3 <token name="@WRAPPER_VERSION@">0.8</token>
4 <xml name="requirements_assembly_post_processor">
5 <requirements>
6 <requirement type="package" version="0.8">plant_tribes_assembly_post_processor</requirement>
7 </requirements>
8 </xml>
9 <xml name="requirements_gene_family_aligner">
10 <requirements>
11 <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement>
12 </requirements>
13 </xml>
14 <xml name="requirements_gene_family_classifier">
15 <requirements>
16 <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement>
17 </requirements>
18 </xml>
19 <xml name="requirements_gene_family_integrator">
20 <requirements>
21 <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
22 </requirements>
23 </xml>
24 <xml name="requirements_kaks_analysis">
25 <requirements>
26 <requirement type="package" version="0.8">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="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
37 </requirements>
38 </xml>
39 <xml name="stdio">
40 <stdio>
41 <exit_code range="1:"/>
42 <exit_code range=":-1"/>
43 <regex match="Error:"/>
44 <regex match="Exception:"/>
45 </stdio>
46 </xml>
47 <xml name="param_codon_alignments">
48 <param name="codon_alignments" type="select" label="Codon alignments">
49 <option value="yes" selected="true">Yes</option>
50 <option value="no">No</option>
51 </param>
52 </xml>
53 <xml name="param_method">
54 <param name="method" type="select" label="Protein clustering method">
55 <option value="gfam" selected="true">GFam</option>
56 <option value="orthofinder">OrthoFinder</option>
57 <option value="orthomcl">OrthoMCL</option>
58 </param>
59 </xml>
60 <xml name="param_options_type">
61 <param name="options_type" type="select" label="Options Configuration">
62 <option value="basic" selected="true">Basic</option>
63 <option value="advanced">Advanced</option>
64 </param>
65 </xml>
66 <xml name="param_orthogroup_fna">
67 <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences">
68 <option value="yes" selected="true">Yes</option>
69 <option value="no">No</option>
70 </param>
71 </xml>
72 <xml name="param_scaffold">
73 <param name="scaffold" type="select" label="Gene family scaffold">
74 <options from_data_table="plant_tribes_scaffolds" />
75 <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." />
76 </param>
77 </xml>
78 <xml name="param_sequence_type">
79 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
80 <option value="protein" selected="true">Amino acid based</option>
81 <option value="dna">Nucleotide based</option>
82 </param>
83 </xml>
84 <xml name="cond_alignment_method">
85 <conditional name="alignment_method_cond">
86 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
87 <option value="mafft" selected="true">MAFFT</option>
88 <option value="pasta">PASTA</option>
89 </param>
90 <when value="mafft" />
91 <when value="pasta">
92 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
93 </when>
94 </conditional>
95 </xml>
96 <xml name="cond_remove_gappy_sequences">
97 <conditional name="remove_gappy_sequences_cond">
98 <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
99 <option value="no" selected="true">No</option>
100 <option value="yes">Yes</option>
101 </param>
102 <when value="no" />
103 <when value="yes">
104 <conditional name="trim_type_cond">
105 <param name="trim_type" type="select" label="Trimming method">
106 <option value="gap_trimming" selected="true">Gap score based trimming</option>
107 <option value="automated_trimming">Automated heuristic trimming</option>
108 </param>
109 <when value="gap_trimming">
110 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
111 </when>
112 <when value="automated_trimming" />
113 </conditional>
114 <conditional name="remove_sequences_with_gaps_cond">
115 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences">
116 <option value="no" selected="true">No</option>
117 <option value="yes">Yes</option>
118 </param>
119 <when value="no" />
120 <when value="yes">
121 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
122 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
123 </when>
124 </conditional>
125 </when>
126 </conditional>
127 </xml>
128 <xml name="citation1">
129 <citation type="bibtex">
130 @misc{None,
131 journal = {None},
132 author = {1. Wafula EK},
133 title = {Manuscript in preparation},
134 year = {None},
135 url = {https://github.com/dePamphilis/PlantTribes},}
136 </citation>
137 </xml>
138 </macros>