Mercurial > repos > greg > kaks_analysis

comparison macros.xml @ 26:73db26d39092 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Tue, 11 Apr 2017 13:36:06 -0400
parents
children f174450ebc44
comparison
equal deleted inserted replaced
25:2c1eb9d63558 26:73db26d39092
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="0.4">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_gene_family_phylogeny_builder">
30 <requirements>
31 <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
32 </requirements>
33 </xml>
34 <xml name="stdio">
35 <stdio>
36 <exit_code range="1:"/>
37 <exit_code range=":-1"/>
38 <regex match="Error:"/>
39 <regex match="Exception:"/>
40 </stdio>
41 </xml>
42 <xml name="param_codon_alignments">
43 <param name="codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
44 <option value="yes" selected="true">Yes</option>
45 <option value="no">No</option>
46 </param>
47 </xml>
48 <xml name="param_method">
49 <param name="method" type="select" label="Protein clustering method">
50 <option value="gfam" selected="true">GFam</option>
51 <option value="orthofinder">OrthoFinder</option>
52 <option value="orthomcl">OrthoMCL</option>
53 </param>
54 </xml>
55 <xml name="param_options_type">
56 <param name="options_type" type="select" label="Options Configuration">
57 <option value="basic" selected="true">Basic</option>
58 <option value="advanced">Advanced</option>
59 </param>
60 </xml>
61 <xml name="param_orthogroup_fna">
62 <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?">
63 <option value="yes" selected="true">Yes</option>
64 <option value="no">No</option>
65 </param>
66 </xml>
67 <xml name="param_scaffold">
68 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
69 <options from_data_table="plant_tribes_scaffolds" />
70 <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." />
71 </param>
72 </xml>
73 <xml name="param_sequence_type">
74 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
75 <option value="protein" selected="true">Amino acid based</option>
76 <option value="dna">Nucleotide based</option>
77 </param>
78 </xml>
79 <xml name="cond_alignment_method">
80 <conditional name="alignment_method_cond">
81 <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
82 <option value="mafft" selected="true">MAFFT algorithm</option>
83 <option value="pasta">PASTA algorithm</option>
84 </param>
85 <when value="mafft" />
86 <when value="pasta">
87 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" />
88 </when>
89 </conditional>
90 </xml>
91 <xml name="cond_remove_gappy_sequences">
92 <conditional name="remove_gappy_sequences_cond">
93 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
94 <option value="no" selected="true">No</option>
95 <option value="yes">Yes</option>
96 </param>
97 <when value="no" />
98 <when value="yes">
99 <conditional name="trim_type_cond">
100 <param name="trim_type" type="select" label="Select process used for trimming">
101 <option value="gap_trimming" selected="true">Remove gappy sites in alignments (gap trimming)</option>
102 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option>
103 </param>
104 <when value="gap_trimming">
105 <param name="gap_trimming" type="float" value="0" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="Zero value has no affect" />
106 </when>
107 <when value="automated_trimming" />
108 </conditional>
109 <conditional name="remove_sequences_with_gaps_cond">
110 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
111 <option value="no" selected="true">No</option>
112 <option value="yes">Yes</option>
113 </param>
114 <when value="no" />
115 <when value="yes">
116 <param name="remove_sequences_with_gaps_of" type="float" value="0" min="0" max="1" label="Remove sequences with gaps of" help="Zero value has no affect" />
117 <param name="iterative_realignment" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
118 </when>
119 </conditional>
120 </when>
121 </conditional>
122 </xml>
123 <xml name="citation1">
124 <citation type="bibtex">
125 @misc{None,
126 journal = {None},
127 author = {1. Wafula EK},
128 title = {Manuscript in preparation},
129 year = {None},
130 url = {https://github.com/dePamphilis/PlantTribes},}
131 </citation>
132 </xml>
133 <xml name="citations2to4">
134 <citation type="bibtex">
135 @article{Sasidharan2012,
136 journal = {Nucleic Acids Research},
137 author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
138 title = {GFam: a platform for automatic annotation of gene families},
139 year = {2012},
140 pages = {gks631},}
141 </citation>
142 <citation type="bibtex">
143 @article{Li2003,
144 journal = {Genome Research}
145 author = {3. Li L, Stoeckert CJ, Roos DS},
146 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
147 year = {2003},
148 volume = {13},
149 number = {9},
150 pages = {2178-2189},}
151 </citation>
152 <citation type="bibtex">
153 @article{Emms2015,
154 journal = {Genome Biology}
155 author = {4. Emms DM, Kelly S},
156 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
157 year = {2015},
158 volume = {16},
159 number = {1},
160 pages = {157},}
161 </citation>
162 </xml>
163 </macros>