Mercurial > repos > greg > phylogenomics_analysis
comparison macros.xml @ 98:56dbe45f4bfb draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 23 Mar 2017 15:01:27 -0400 |
| parents | 7389c8a99491 |
| children | de42cdf6e10b |
comparison
equal
deleted
inserted
replaced
| 97:7389c8a99491 | 98:56dbe45f4bfb |
|---|---|
| 11 <exit_code range=":-1"/> | 11 <exit_code range=":-1"/> |
| 12 <regex match="Error:"/> | 12 <regex match="Error:"/> |
| 13 <regex match="Exception:"/> | 13 <regex match="Exception:"/> |
| 14 </stdio> | 14 </stdio> |
| 15 </xml> | 15 </xml> |
| 16 <token name="@REMOVE_GAPPY_SEQUENCES_COND@"> | |
| 17 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond | |
| 18 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences | |
| 19 #if str($remove_gappy_sequences) == 'no': | |
| 20 #set multiple_sequence_alignments_cond = $remove_gappy_sequences_cond.multiple_sequence_alignments_cond | |
| 21 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments | |
| 22 #if str($multiple_sequence_alignments) == 'yes': | |
| 23 #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond | |
| 24 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option | |
| 25 #if str($multiple_sequence_alignments_option) == 'pasta_alignments': | |
| 26 #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit | |
| 27 #end if | |
| 28 #end if | |
| 29 #else: | |
| 30 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond | |
| 31 #set trim_type = $trim_type_cond.trim_type | |
| 32 #if str($trim_type) == 'gap_trimming': | |
| 33 #set gap_trimming = $trim_type_cond.gap_trimming | |
| 34 #end if | |
| 35 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond | |
| 36 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps | |
| 37 #if str($remove_sequences_with_gaps) == 'no': | |
| 38 #set multiple_sequence_alignments_cond = $remove_sequences_with_gaps_cond.multiple_sequence_alignments_cond | |
| 39 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments | |
| 40 #if str($multiple_sequence_alignments) == 'yes': | |
| 41 #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond | |
| 42 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option | |
| 43 #if str($multiple_sequence_alignments_option) == 'pasta_alignments': | |
| 44 #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit | |
| 45 #end if | |
| 46 #end if | |
| 47 #else: | |
| 48 #set remove_sequences_with_gaps_of = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of | |
| 49 #set multiple_sequence_alignments_cond = $remove_sequences_with_gaps_cond.multiple_sequence_alignments_cond | |
| 50 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments | |
| 51 #if str($multiple_sequence_alignments) == 'yes': | |
| 52 #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond | |
| 53 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option | |
| 54 #if str($multiple_sequence_alignments_option) == 'pasta_alignments': | |
| 55 #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit | |
| 56 #else if str($multiple_sequence_alignments_option) == 'iterative_realignments': | |
| 57 #set iterative_realignments = $multiple_sequence_alignments_option_cond.iterative_realignments | |
| 58 #end if | |
| 59 #end if | |
| 60 #end if | |
| 61 #end if | |
| 62 </token> | |
| 63 <token name="@SET_PHYLOGENETIC_TREES@"> | |
| 64 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond | |
| 65 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees | |
| 66 </token> | |
| 67 <token name="@TREE_INFERENCE_COND@"> | |
| 68 #set tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond | |
| 69 #set tree_inference = $tree_inference_cond.tree_inference | |
| 70 #if str($tree_inference) == 'raxml': | |
| 71 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond | |
| 72 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file | |
| 73 #if str($rooting_order_file) == 'yes': | |
| 74 #set rooting_order = $rooting_order_file_cond.rooting_order | |
| 75 #end if | |
| 76 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates | |
| 77 #end if | |
| 78 #set max_orthogroup_size = $phylogenetic_trees_cond.max_orthogroup_size | |
| 79 #set min_orthogroup_size = $phylogenetic_trees_cond.min_orthogroup_size | |
| 80 </token> | |
| 16 <xml name="param_scaffold"> | 81 <xml name="param_scaffold"> |
| 17 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> | 82 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> |
| 18 <options from_data_table="plant_tribes_scaffolds" /> | 83 <options from_data_table="plant_tribes_scaffolds" /> |
| 19 <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." /> | 84 <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." /> |
| 20 </param> | 85 </param> |
| 200 <conditional name="trim_type_cond"> | 265 <conditional name="trim_type_cond"> |
| 201 <param name="trim_type" type="select" label="Select process used for gap trimming"> | 266 <param name="trim_type" type="select" label="Select process used for gap trimming"> |
| 202 <option value="gap_trimming" selected="true">Nucleotide based </option> | 267 <option value="gap_trimming" selected="true">Nucleotide based </option> |
| 203 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option> | 268 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option> |
| 204 </param> | 269 </param> |
| 205 <when value="automated_trimming" /> | |
| 206 <when value="gap_trimming"> | 270 <when value="gap_trimming"> |
| 207 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps" /> | 271 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps" /> |
| 208 </when> | 272 </when> |
| 273 <when value="automated_trimming" /> | |
| 209 </conditional> | 274 </conditional> |
| 210 <conditional name="remove_sequences_with_gaps_cond"> | 275 <conditional name="remove_sequences_with_gaps_cond"> |
| 211 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?"> | 276 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?"> |
| 212 <option value="no" selected="true">No</option> | 277 <option value="no" selected="true">No</option> |
| 213 <option value="yes">Yes</option> | 278 <option value="yes">Yes</option> |