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comparison macros.xml @ 8:87e2450855c2 draft

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author greg
date Fri, 28 Apr 2017 09:14:26 -0400
parents 1d178e90fbe6
children 2457321db163
comparison
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7:0bf47f620170 8:87e2450855c2
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@">0.8</token> 3 <token name="@WRAPPER_VERSION@">0.8</token>
4 <xml name="requirements_assembly_post_processor"> 4 <xml name="requirements_assembly_post_processor">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement> 6 <requirement type="package" version="0.8">plant_tribes_assembly_post_processor</requirement>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
9 <xml name="requirements_gene_family_aligner"> 9 <xml name="requirements_gene_family_aligner">
10 <requirements> 10 <requirements>
11 <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement> 11 <requirement type="package" version="0.8">plant_tribes_gene_family_aligner</requirement>
57 <option value="basic" selected="true">Basic</option> 57 <option value="basic" selected="true">Basic</option>
58 <option value="advanced">Advanced</option> 58 <option value="advanced">Advanced</option>
59 </param> 59 </param>
60 </xml> 60 </xml>
61 <xml name="param_orthogroup_fna"> 61 <xml name="param_orthogroup_fna">
62 <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?"> 62 <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences?">
63 <option value="yes" selected="true">Yes</option> 63 <option value="yes" selected="true">Yes</option>
64 <option value="no">No</option> 64 <option value="no">No</option>
65 </param> 65 </param>
66 </xml> 66 </xml>
67 <xml name="param_scaffold"> 67 <xml name="param_scaffold">
68 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 68 <param name="scaffold" type="select" label="Gene family scaffold">
69 <options from_data_table="plant_tribes_scaffolds" /> 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." /> 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> 71 </param>
72 </xml> 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>
73 <xml name="cond_alignment_method"> 79 <xml name="cond_alignment_method">
74 <conditional name="alignment_method_cond"> 80 <conditional name="alignment_method_cond">
75 <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments"> 81 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
76 <option value="mafft" selected="true">MAFFT algorithm</option> 82 <option value="mafft" selected="true">MAFFT</option>
77 <option value="pasta">PASTA algorithm</option> 83 <option value="pasta">PASTA</option>
78 </param> 84 </param>
79 <when value="mafft" /> 85 <when value="mafft" />
80 <when value="pasta"> 86 <when value="pasta">
81 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" /> 87 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" />
82 </when> 88 </when>
83 </conditional> 89 </conditional>
84 </xml> 90 </xml>
85 <xml name="cond_remove_gappy_sequences"> 91 <xml name="cond_remove_gappy_sequences">
86 <conditional name="remove_gappy_sequences_cond"> 92 <conditional name="remove_gappy_sequences_cond">
87 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?"> 93 <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration?">
88 <option value="no" selected="true">No</option> 94 <option value="no" selected="true">No</option>
89 <option value="yes">Yes</option> 95 <option value="yes">Yes</option>
90 </param> 96 </param>
91 <when value="no" /> 97 <when value="no" />
92 <when value="yes"> 98 <when value="yes">
93 <conditional name="trim_type_cond"> 99 <conditional name="trim_type_cond">
94 <param name="trim_type" type="select" label="Select process used for gap trimming"> 100 <param name="trim_type" type="select" label="Trimming method">
95 <option value="gap_trimming" selected="true">Nucleotide based</option> 101 <option value="gap_trimming" selected="true">Gap score based trimming</option>
96 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option> 102 <option value="automated_trimming">Automated heuristic trimming</option>
97 </param> 103 </param>
98 <when value="gap_trimming"> 104 <when value="gap_trimming">
99 <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" /> 105 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
100 </when> 106 </when>
101 <when value="automated_trimming" /> 107 <when value="automated_trimming" />
102 </conditional> 108 </conditional>
103 <conditional name="remove_sequences_with_gaps_cond"> 109 <conditional name="remove_sequences_with_gaps_cond">
104 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?"> 110 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences?">
105 <option value="no" selected="true">No</option> 111 <option value="no" selected="true">No</option>
106 <option value="yes">Yes</option> 112 <option value="yes">Yes</option>
107 </param> 113 </param>
108 <when value="no" /> 114 <when value="no" />
109 <when value="yes"> 115 <when value="yes">
110 <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" /> 116 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
111 <param name="iterative_realignment" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/> 117 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
112 </when> 118 </when>
113 </conditional> 119 </conditional>
114 </when> 120 </when>
115 </conditional> 121 </conditional>
116 </xml> 122 </xml>
122 title = {Manuscript in preparation}, 128 title = {Manuscript in preparation},
123 year = {None}, 129 year = {None},
124 url = {https://github.com/dePamphilis/PlantTribes},} 130 url = {https://github.com/dePamphilis/PlantTribes},}
125 </citation> 131 </citation>
126 </xml> 132 </xml>
127 <xml name="citations2to4">
128 <citation type="bibtex">
129 @article{Sasidharan2012,
130 journal = {Nucleic Acids Research},
131 author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
132 title = {GFam: a platform for automatic annotation of gene families},
133 year = {2012},
134 pages = {gks631},}
135 </citation>
136 <citation type="bibtex">
137 @article{Li2003,
138 journal = {Genome Research}
139 author = {3. Li L, Stoeckert CJ, Roos DS},
140 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
141 year = {2003},
142 volume = {13},
143 number = {9},
144 pages = {2178-2189},}
145 </citation>
146 <citation type="bibtex">
147 @article{Emms2015,
148 journal = {Genome Biology}
149 author = {4. Emms DM, Kelly S},
150 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
151 year = {2015},
152 volume = {16},
153 number = {1},
154 pages = {157},}
155 </citation>
156 </xml>
157 </macros> 133 </macros>