Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 78:86b95e576d32 draft

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author greg
date Wed, 22 Mar 2017 11:36:32 -0400
parents 60d375f35e24
children e528feaa44bd
comparison
equal deleted inserted replaced
77:98c2a9f97e83 78:86b95e576d32
18 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments 18 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
19 #if str($multiple_sequence_alignments) == 'yes': 19 #if str($multiple_sequence_alignments) == 'yes':
20 #set multiple_sequence_alignments_option_cond = $options_type_cond.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond 20 #set multiple_sequence_alignments_option_cond = $options_type_cond.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
21 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option 21 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
22 #end if 22 #end if
23 #set phylogenomic_trees_cond = $options_type_cond.phylogenetic_trees_cond 23 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond
24 #set phylogenetic_trees = $phylogenomic_trees_cond.phylogenetic_trees 24 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees
25 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond 25 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
26 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences 26 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
27 #end if 27 #end if
28 28
29 python $__tool_directory__/phylogenomics_analysis.py 29 python $__tool_directory__/phylogenomics_analysis.py
121 <conditional name="options_type_cond"> 121 <conditional name="options_type_cond">
122 <expand macro="param_options_type" /> 122 <expand macro="param_options_type" />
123 <when value="basic" /> 123 <when value="basic" />
124 <when value="advanced"> 124 <when value="advanced">
125 <expand macro="cond_multiple_sequence_alignments" /> 125 <expand macro="cond_multiple_sequence_alignments" />
126 <expand macro="cond_phylogenomic_trees_ptortho" />
127 <expand macro="cond_remove_gappy_sequences" /> 126 <expand macro="cond_remove_gappy_sequences" />
128 </when> 127 </when>
129 </conditional> 128 </conditional>
130 </when> 129 </when>
131 <when value="ptorthocs"> 130 <when value="ptorthocs">
135 <conditional name="options_type_cond"> 134 <conditional name="options_type_cond">
136 <expand macro="param_options_type" /> 135 <expand macro="param_options_type" />
137 <when value="basic" /> 136 <when value="basic" />
138 <when value="advanced"> 137 <when value="advanced">
139 <expand macro="cond_multiple_sequence_alignments" /> 138 <expand macro="cond_multiple_sequence_alignments" />
140 <expand macro="cond_phylogenomic_trees_ptorthocs" />
141 <expand macro="cond_remove_gappy_sequences" /> 139 <expand macro="cond_remove_gappy_sequences" />
142 <expand macro="param_multiple_codon_alignments" /> 140 <expand macro="param_multiple_codon_alignments" />
143 </when> 141 </when>
144 </conditional> 142 </conditional>
145 </when> 143 </when>