Mercurial > repos > greg > phylogenomics_analysis
comparison macros.xml @ 105:e0fa1e2105f6 draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 27 Mar 2017 11:20:26 -0400 |
| parents | 4d78ec10c07e |
| children | 5e5db789406a |
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| 104:4d78ec10c07e | 105:e0fa1e2105f6 |
|---|---|
| 126 #end if | 126 #end if |
| 127 --bootstrap_replicates $bootstrap_replicates | 127 --bootstrap_replicates $bootstrap_replicates |
| 128 #end if | 128 #end if |
| 129 --min_orthogroup_size $min_orthogroup_size | 129 --min_orthogroup_size $min_orthogroup_size |
| 130 --max_orthogroup_size $max_orthogroup_size | 130 --max_orthogroup_size $max_orthogroup_size |
| 131 </token> | |
| 132 <token name="@OUTPUT_ALN@"> | |
| 133 #if str($input_format_cond['options_type_cond']['options_type']) == 'advanced' and ((str($input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['remove_gappy_sequences']) == 'yes' and str($input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments']) == 'yes') or (str($input_format_cond['options_type_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes') and str($input_format_cond['options_type_cond']['remove_sequences_with_gaps_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments']) == 'yes')): | |
| 134 --output_aln '$output_aln' | |
| 135 --output_aln_dir '$output_aln.files_path' | |
| 136 #end if | |
| 137 </token> | |
| 138 <token name="@OUTPUT_TREE@"> | |
| 139 #if str($input_format_cond['options_type_cond']['options_type']) == 'advanced' and str($input_format_cond['options_type_cond']['phylogenetic_trees_cond']['phylogenetic_trees']) == 'yes': | |
| 140 --output_tree '$output_tree' | |
| 141 --output_tree_dir '$output_tree.files_path' | |
| 142 #end if | |
| 131 </token> | 143 </token> |
| 132 <xml name="param_scaffold"> | 144 <xml name="param_scaffold"> |
| 133 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> | 145 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> |
| 134 <options from_data_table="plant_tribes_scaffolds" /> | 146 <options from_data_table="plant_tribes_scaffolds" /> |
| 135 <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." /> | 147 <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." /> |