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comparison macros.xml @ 90:6c1cfd0be856 draft

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Uploaded
author greg
date Thu, 23 Mar 2017 08:30:55 -0400
parents 0fc75cdc686a
children 79573009efe0
comparison
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89:0fc75cdc686a 90:6c1cfd0be856
59 </when> 59 </when>
60 </conditional> 60 </conditional>
61 </when> 61 </when>
62 </conditional> 62 </conditional>
63 </xml> 63 </xml>
64 <xml name="param_multiple_sequence_alignments">
65 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
66 <option value="no" selected="true">No</option>
67 <option value="yes">Yes</option>
68 </param>
69 </xml>
70 <xml name="param_multiple_sequence_alignments_option">
71 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments">
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>
74 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
75 </param>
76 </xml>
77 <xml name="whens_multiple_sequence_alignments_option_cond">
78 <when value="create_alignments" />
79 <when value="add_alignments" />
80 <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" />
82 </when>
83 </xml>
64 <xml name="cond_multiple_sequence_alignments"> 84 <xml name="cond_multiple_sequence_alignments">
65 <conditional name="multiple_sequence_alignments_cond"> 85 <conditional name="multiple_sequence_alignments_cond">
66 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?"> 86 <expand macro="param_multiple_sequence_alignments" />
67 <option value="no" selected="true">No</option>
68 <option value="yes">Yes</option>
69 </param>
70 <when value="no" /> 87 <when value="no" />
71 <when value="yes"> 88 <when value="yes">
72 <conditional name="multiple_sequence_alignments_option_cond"> 89 <conditional name="multiple_sequence_alignments_option_cond">
73 <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments"> 90 <expand macro="whens_multiple_sequence_alignments_option_cond" />
74 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option> 91 <expand macro="param_multiple_sequence_alignments_option" />
75 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
76 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
77 </param>
78 <when value="create_alignments" />
79 <when value="add_alignments" />
80 <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" />
82 </when>
83 </conditional> 92 </conditional>
84 </when> 93 </when>
85 </conditional> 94 </conditional>
86 </xml> 95 </xml>
87 <xml name="cond_phylogenetic_trees_ptortho"> 96 <xml name="cond_phylogenetic_trees_ptortho">