Mercurial > repos > greg > gene_family_integrator

comparison macros.xml @ 27:346dc0d9af6f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 05 Oct 2017 14:21:14 -0400
parents b91bf5a51d38
children 68da6cc1c6c0
comparison
equal deleted inserted replaced
26:b91bf5a51d38 27:346dc0d9af6f
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_scaffold"> 11 <xml name="param_scaffold">
59 <param name="scaffold" type="select" label="Gene family scaffold"> 12 <param name="scaffold" type="select" label="Gene family scaffold">
60 <options from_data_table="plant_tribes_scaffolds" /> 13 <options from_data_table="plant_tribes_scaffolds" />
61 <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." />
62 </param> 15 </param>
63 </xml>
64 <xml name="cond_alignment_method">
65 <conditional name="alignment_method_cond">
66 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
67 <option value="mafft" selected="true">MAFFT</option>
68 <option value="pasta">PASTA</option>
69 </param>
70 <when value="mafft" />
71 <when value="pasta">
72 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
73 </when>
74 </conditional>
75 </xml>
76 <xml name="cond_remove_gappy_sequences">
77 <conditional name="remove_gappy_sequences_cond">
78 <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
79 <option value="no" selected="true">No</option>
80 <option value="yes">Yes</option>
81 </param>
82 <when value="no" />
83 <when value="yes">
84 <conditional name="trim_type_cond">
85 <param name="trim_type" type="select" label="Trimming method">
86 <option value="gap_trimming" selected="true">Gap score based trimming</option>
87 <option value="automated_trimming">Automated heuristic trimming</option>
88 </param>
89 <when value="gap_trimming">
90 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
91 </when>
92 <when value="automated_trimming" />
93 </conditional>
94 <conditional name="remove_sequences_with_gaps_cond">
95 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences">
96 <option value="no" selected="true">No</option>
97 <option value="yes">Yes</option>
98 </param>
99 <when value="no" />
100 <when value="yes">
101 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
102 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
103 </when>
104 </conditional>
105 <param name="output_pristine_alignments" type="select" display="radio" label="Output non-filtered, non-trimmed alignemnts?" help="In addition to trimmed/filtered alignments">
106 <option value="no" selected="true">No</option>
107 <option value="yes">Yes</option>
108 </param>
109 </when>
110 </conditional>
111 </xml> 16 </xml>
112 <xml name="citation1"> 17 <xml name="citation1">
113 <citation type="bibtex"> 18 <citation type="bibtex">
114 @misc{None, 19 @misc{None,
115 journal = {None}, 20 journal = {None},