Mercurial > repos > greg > phylogenomics_analysis

comparison macros.xml @ 74:7170b072b40a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Wed, 22 Mar 2017 11:20:53 -0400
parents 0f498f13f109
children 063a39e39705
comparison
equal deleted inserted replaced
73:7363c4e9423c 74:7170b072b40a
53 </when> 53 </when>
54 </conditional> 54 </conditional>
55 </when> 55 </when>
56 </conditional> 56 </conditional>
57 </xml> 57 </xml>
58 <xml name="cond_phylogenomic_trees"> 58 <xml name="cond_phylogenomic_trees_start">
59 <conditional name="phylogenetic_trees_cond"> 59 <conditional name="phylogenetic_trees_cond">
60 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?"> 60 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
61 <option value="no" selected="true">No</option> 61 <option value="no" selected="true">No</option>
62 <option value="yes">Yes</option> 62 <option value="yes">Yes</option>
63 </param> 63 </param>
83 </when> 83 </when>
84 <when value="fasttree" /> 84 <when value="fasttree" />
85 </conditional> 85 </conditional>
86 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" /> 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" /> 87 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
88 </xml>
89 <xml name="param_sequence_type">
90 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
91 <option value="protein" selected="true">Amino acid based</option>
92 <option value="dna">Nucleotide based</option>
93 </param>
94 </xml>
95 <xml name="cond_phylogenomic_trees_end">
88 </when> 96 </when>
89 </conditional> 97 </conditional>
90 </xml> 98 </xml>
91 <xml name="cond_remove_gappy_sequences"> 99 <xml name="cond_remove_gappy_sequences">
92 <conditional name="remove_gappy_sequences_cond"> 100 <conditional name="remove_gappy_sequences_cond">
118 </when> 126 </when>
119 </conditional> 127 </conditional>
120 </when> 128 </when>
121 </conditional> 129 </conditional>
122 </xml> 130 </xml>
123 <xml name="cond_multiple_codon_alignments"> 131 <xml name="param_multiple_codon_alignments">
124 <conditional name="multiple_codon_alignments_cond"> 132 <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
125 <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?"> 133 <option value="no" selected="True">No</option>
126 <option value="no" selected="True">No</option> 134 <option value="yes">Yes</option>
127 <option value="yes">Yes</option> 135 </param>
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> 136 </xml>
138 <xml name="citations"> 137 <xml name="citations">
139 <citations> 138 <citations>
140 <citation type="bibtex"> 139 <citation type="bibtex">
141 @misc{None, 140 @misc{None,