Mercurial > repos > greg > phylogenomics_analysis
comparison phylogenomics_analysis.xml @ 76:60d375f35e24 draft
Uploaded
author | greg |
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date | Wed, 22 Mar 2017 11:29:27 -0400 |
parents | 7363c4e9423c |
children | 86b95e576d32 |
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75:063a39e39705 | 76:60d375f35e24 |
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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> |