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comparison macros.xml @ 91:79573009efe0 draft

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author greg
date Thu, 23 Mar 2017 08:51:36 -0400
parents 6c1cfd0be856
children ed9cd83a0236
comparison
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90:6c1cfd0be856 91:79573009efe0
72 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option> 72 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
73 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option> 73 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
74 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option> 74 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
75 </param> 75 </param>
76 </xml> 76 </xml>
77 <xml name="cond_multiple_sequence_alignments_option_with_iterative_realignments">
78 <conditional name="multiple_sequence_alignments_option_cond">
79 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
80 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
81 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
82 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
83 <option value="iterative_realignments">Iterative orthogroups realignment, trimming and fitering</option>
84 </param>
85 <expand macro="whens_multiple_sequence_alignments_option_cond" />
86 <when value="iterative_realignments">
87 <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/>
88 </when>
89 </conditional>
90 </xml>
77 <xml name="whens_multiple_sequence_alignments_option_cond"> 91 <xml name="whens_multiple_sequence_alignments_option_cond">
78 <when value="create_alignments" /> 92 <when value="create_alignments" />
79 <when value="add_alignments" /> 93 <when value="add_alignments" />
80 <when value="pasta_alignments"> 94 <when value="pasta_alignments">
81 <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iterations that the PASTA algorithm will execute" /> 95 <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iterations that the PASTA algorithm will execute" />
87 <when value="no" /> 101 <when value="no" />
88 <when value="yes"> 102 <when value="yes">
89 <conditional name="multiple_sequence_alignments_option_cond"> 103 <conditional name="multiple_sequence_alignments_option_cond">
90 <expand macro="whens_multiple_sequence_alignments_option_cond" /> 104 <expand macro="whens_multiple_sequence_alignments_option_cond" />
91 <expand macro="param_multiple_sequence_alignments_option" /> 105 <expand macro="param_multiple_sequence_alignments_option" />
106 </conditional>
107 </when>
108 </conditional>
109 </xml>
110 <xml name="cond_multiple_sequence_alignments_with_iterative_realignments">
111 <conditional name="multiple_sequence_alignments_cond">
112 <expand macro="param_multiple_sequence_alignments" />
113 <when value="no" />
114 <when value="yes">
115 <conditional name="multiple_sequence_alignments_option_cond">
116 <expand macro="whens_multiple_sequence_alignments_option_cond" />
117 <expand macro="param_multiple_sequence_alignments_option_with_iterative_realignments" />
92 </conditional> 118 </conditional>
93 </when> 119 </when>
94 </conditional> 120 </conditional>
95 </xml> 121 </xml>
96 <xml name="cond_phylogenetic_trees_ptortho"> 122 <xml name="cond_phylogenetic_trees_ptortho">
186 <conditional name="remove_sequences_with_gaps_cond"> 212 <conditional name="remove_sequences_with_gaps_cond">
187 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?"> 213 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
188 <option value="no" selected="true">No</option> 214 <option value="no" selected="true">No</option>
189 <option value="yes">Yes</option> 215 <option value="yes">Yes</option>
190 </param> 216 </param>
191 <when value="no" /> 217 <when value="no">
218 <expand macro="cond_multiple_sequence_alignments" />
219 </when>
192 <when value="yes"> 220 <when value="yes">
193 <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" /> 221 <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" />
194 <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/> 222 <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/>
195 <expand macro="cond_multiple_sequence_alignments" /> 223 <expand macro="cond_multiple_sequence_alignments_with_iterative_realignments" />
196 </when> 224 </when>
197 </conditional> 225 </conditional>
198 <expand macro="cond_multiple_sequence_alignments" />
199 </when> 226 </when>
200 </conditional> 227 </conditional>
201 </xml> 228 </xml>
202 <xml name="param_multiple_codon_alignments"> 229 <xml name="param_multiple_codon_alignments">
203 <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?"> 230 <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">