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comparison phylogenomics_analysis.xml @ 76:60d375f35e24 draft

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Uploaded
author greg
date Wed, 22 Mar 2017 11:29:27 -0400
parents 7363c4e9423c
children 86b95e576d32
comparison
equal deleted inserted replaced
75:063a39e39705 76:60d375f35e24
31 #if str($input_format) == 'ptortho': 31 #if str($input_format) == 'ptortho':
32 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 32 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
33 #else: 33 #else:
34 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 34 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
35 --orthogroup_fna 'true' 35 --orthogroup_fna 'true'
36 #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond 36 #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments
37 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
38 #if str($multiple_codon_alignments) == 'yes': 37 #if str($multiple_codon_alignments) == 'yes':
39 --sequence_type $multiple_codon_alignments_cond.sequence_type 38 --codon_alignments 'true'
40 #end if 39 #end if
41 #end if 40 #end if
42 --config_dir '$scaffold.fields.path' 41 --config_dir '$scaffold.fields.path'
43 --scaffold '$scaffold.fields.path' 42 --scaffold '$scaffold.fields.path'
44 --method $method 43 --method $method
66 #end if 65 #end if
67 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates 66 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
68 #end if 67 #end if
69 --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size 68 --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size
70 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size 69 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size
70 #if str($input_format) == 'ptortho':
71 --sequence_type 'protein'
72 #else:
73 --sequence_type $phylogenetic_trees_cond.sequence_type
74 #end if
71 #end if 75 #end if
72 76
73 #if str($remove_gappy_sequences) == 'yes': 77 #if str($remove_gappy_sequences) == 'yes':
74 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond 78 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
75 #set trim_type = $trim_type_cond.trim_type 79 #set trim_type = $trim_type_cond.trim_type
117 <conditional name="options_type_cond"> 121 <conditional name="options_type_cond">
118 <expand macro="param_options_type" /> 122 <expand macro="param_options_type" />
119 <when value="basic" /> 123 <when value="basic" />
120 <when value="advanced"> 124 <when value="advanced">
121 <expand macro="cond_multiple_sequence_alignments" /> 125 <expand macro="cond_multiple_sequence_alignments" />
122 <expand macro="cond_phylogenomic_trees" /> 126 <expand macro="cond_phylogenomic_trees_ptortho" />
123 <expand macro="cond_remove_gappy_sequences" /> 127 <expand macro="cond_remove_gappy_sequences" />
124 </when> 128 </when>
125 </conditional> 129 </conditional>
126 </when> 130 </when>
127 <when value="ptorthocs"> 131 <when value="ptorthocs">
131 <conditional name="options_type_cond"> 135 <conditional name="options_type_cond">
132 <expand macro="param_options_type" /> 136 <expand macro="param_options_type" />
133 <when value="basic" /> 137 <when value="basic" />
134 <when value="advanced"> 138 <when value="advanced">
135 <expand macro="cond_multiple_sequence_alignments" /> 139 <expand macro="cond_multiple_sequence_alignments" />
136 <expand macro="cond_phylogenomic_trees" /> 140 <expand macro="cond_phylogenomic_trees_ptorthocs" />
137 <expand macro="cond_remove_gappy_sequences" /> 141 <expand macro="cond_remove_gappy_sequences" />
138 <expand macro="cond_multiple_codon_alignments" /> 142 <expand macro="param_multiple_codon_alignments" />
139 </when> 143 </when>
140 </conditional> 144 </conditional>
141 </when> 145 </when>
142 </conditional> 146 </conditional>
143 </inputs> 147 </inputs>