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comparison macros.xml @ 72:0f498f13f109 draft

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author greg
date Wed, 22 Mar 2017 10:38:45 -0400
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71:43e5db9461cf 72:0f498f13f109
1 <?xml version='1.0' encoding='UTF-8'?>
2 <macros>
3 <xml name="requirements">
4 <requirements>
5 <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement>
6 </requirements>
7 </xml>
8 <xml name="stdio">
9 <stdio>
10 <exit_code range="1:"/>
11 <exit_code range=":-1"/>
12 <regex match="Error:"/>
13 <regex match="Exception:"/>
14 </stdio>
15 </xml>
16 <xml name="param_scaffold">
17 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
18 <options from_data_table="plant_tribes_scaffolds" />
19 <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." />
20 </param>
21 </xml>
22 <xml name="param_method">
23 <param name="method" type="select" label="Protein clustering method">
24 <option value="gfam" selected="true">GFam</option>
25 <option value="orthofinder">OrthoFinder</option>
26 <option value="orthomcl">OrthoMCL</option>
27 </param>
28 </xml>
29 <xml name="param_options_type">
30 <param name="options_type" type="select" label="Options Configuration">
31 <option value="basic" selected="true">Basic</option>
32 <option value="advanced">Advanced</option>
33 </param>
34 </xml>
35 <xml name="cond_multiple_sequence_alignments">
36 <conditional name="multiple_sequence_alignments_cond">
37 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
38 <option value="no" selected="true">No</option>
39 <option value="yes">Yes</option>
40 </param>
41 <when value="no" />
42 <when value="yes">
43 <conditional name="multiple_sequence_alignments_option_cond">
44 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
45 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
46 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
47 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
48 </param>
49 <when value="create_alignments" />
50 <when value="add_alignments" />
51 <when value="pasta_alignments">
52 <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iterations that the PASTA algorithm will execute" />
53 </when>
54 </conditional>
55 </when>
56 </conditional>
57 </xml>
58 <xml name="cond_phylogenomic_trees">
59 <conditional name="phylogenetic_trees_cond">
60 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
61 <option value="no" selected="true">No</option>
62 <option value="yes">Yes</option>
63 </param>
64 <when value="no" />
65 <when value="yes">
66 <conditional name="tree_inference_cond">
67 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
68 <option value="raxml" selected="true">RAxML</option>
69 <option value="fasttree">FastTree</option>
70 </param>
71 <when value="raxml">
72 <conditional name="rooting_order_file_cond">
73 <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
74 <option value="no" selected="true">No</option>
75 <option value="yes">Yes</option>
76 </param>
77 <when value="no" />
78 <when value="yes">
79 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
80 </when>
81 </conditional>
82 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
83 </when>
84 <when value="fasttree" />
85 </conditional>
86 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
87 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
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 gap trimming">
101 <option value="gap_trimming" selected="true">Nucleotide based </option>
102 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
103 </param>
104 <when value="automated_trimming" />
105 <when value="gap_trimming">
106 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps" />
107 </when>
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="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" />
117 <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/>
118 </when>
119 </conditional>
120 </when>
121 </conditional>
122 </xml>
123 <xml name="cond_multiple_codon_alignments">
124 <conditional name="multiple_codon_alignments_cond">
125 <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
126 <option value="no" selected="True">No</option>
127 <option value="yes">Yes</option>
128 </param>
129 <when value="no" />
130 <when value="yes">
131 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
132 <option value="protein" selected="true">Amino acid based</option>
133 <option value="dna">Nucleotide based</option>
134 </param>
135 </when>
136 </conditional>
137 </xml>
138 <xml name="citations">
139 <citations>
140 <citation type="bibtex">
141 @misc{None,
142 journal = {None},
143 author = {1. Wafula EK},
144 title = {Manuscript in preparation},
145 year = {None},
146 url = {https://github.com/dePamphilis/PlantTribes},}
147 </citation>
148 <citation type="bibtex">
149 @article{Mirarab2014,
150 journal = {Research in Computational Molecular Biology (RECOMB)},
151 author = {2. Mirarab S, Nguyen N, Warnow T},
152 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan (Ed.)},
153 year = {2014},
154 pages = {177–191},
155 url = {https://github.com/smirarab/pasta},}
156 </citation>
157 <citation type="bibtex">
158 @article{Salvador2009,
159 journal = {Bioinformatics},
160 author = {3. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T},
161 title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses},
162 year = {2009},
163 url = {http://trimal.cgenomics.org},}
164 </citation>
165 <citation type="bibtex">
166 @article{Stamatakis2014,
167 journal = {Bioinformatics},
168 author = {4. Stamatakis A},
169 title = {RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies},
170 year = {2014},
171 url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html},}
172 </citation>
173 <citation type="doi">10.1371/journal.pone.0009490</citation>
174 <citation type="doi">10.1093/bioinformatics/btw412</citation>
175 </citations>
176 </xml>
177 </macros>