Mercurial > repos > greg > gene_family_aligner

comparison macros.xml @ 14:af8dad310c32 draft

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author greg
date Tue, 11 Apr 2017 14:21:35 -0400
parents a2b29eb5459d
children 4a0837f2b995
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13:d7e6201b8d81 14:af8dad310c32
68 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 68 <param name="scaffold" type="select" label="Orthogroups or gene families proteins 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="Select method for multiple sequence alignments">
76 <option value="mafft" selected="true">MAFFT algorithm</option> 82 <option value="mafft" selected="true">MAFFT algorithm</option>
77 <option value="pasta">PASTA algorithm</option> 83 <option value="pasta">PASTA algorithm</option>
94 <param name="trim_type" type="select" label="Select process used for trimming"> 100 <param name="trim_type" type="select" label="Select process used for trimming">
95 <option value="gap_trimming" selected="true">Remove gappy sites in alignments (gap trimming)</option> 101 <option value="gap_trimming" selected="true">Remove gappy sites in alignments (gap trimming)</option>
96 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option> 102 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated 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="Remove sites in alignments with gaps of" />
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 with specified gaps?">
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="Remove sequences with gaps of" />
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="Maximum number of iterations" />
112 </when> 118 </when>
113 </conditional> 119 </conditional>
114 </when> 120 </when>
115 </conditional> 121 </conditional>
116 </xml> 122 </xml>