Mercurial > repos > greg > phylogenomics_analysis
comparison macros.xml @ 88:5f64fcf4437a draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 23 Mar 2017 08:16:27 -0400 |
| parents | 7d2bb431c8c2 |
| children | 0fc75cdc686a |
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| 87:6154253af263 | 88:5f64fcf4437a |
|---|---|
| 41 <when value="yes"> | 41 <when value="yes"> |
| 42 <conditional name="options_type_cond"> | 42 <conditional name="options_type_cond"> |
| 43 <expand macro="param_options_type" /> | 43 <expand macro="param_options_type" /> |
| 44 <when value="basic" /> | 44 <when value="basic" /> |
| 45 <when value="advanced"> | 45 <when value="advanced"> |
| 46 <expand macro="cond_multiple_sequence_alignments" /> | 46 <expand macro="cond_remove_gappy_sequences" /> |
| 47 <expand macro="cond_phylogenetic_trees_ptorthocs" /> | 47 <expand macro="cond_phylogenetic_trees_ptorthocs" /> |
| 48 <expand macro="cond_remove_gappy_sequences" /> | |
| 49 <expand macro="param_multiple_codon_alignments" /> | 48 <expand macro="param_multiple_codon_alignments" /> |
| 50 </when> | 49 </when> |
| 51 </conditional> | 50 </conditional> |
| 52 </when> | 51 </when> |
| 53 <when value="no"> | 52 <when value="no"> |
| 54 <conditional name="options_type_cond"> | 53 <conditional name="options_type_cond"> |
| 55 <expand macro="param_options_type" /> | 54 <expand macro="param_options_type" /> |
| 56 <when value="basic" /> | 55 <when value="basic" /> |
| 57 <when value="advanced"> | 56 <when value="advanced"> |
| 58 <expand macro="cond_multiple_sequence_alignments" /> | 57 <expand macro="cond_remove_gappy_sequences" /> |
| 59 <expand macro="cond_phylogenetic_trees_ptorthocs" /> | 58 <expand macro="cond_phylogenetic_trees_ptorthocs" /> |
| 60 <expand macro="cond_remove_gappy_sequences" /> | |
| 61 </when> | 59 </when> |
| 62 </conditional> | 60 </conditional> |
| 63 </when> | 61 </when> |
| 64 </conditional> | 62 </conditional> |
| 65 </xml> | 63 </xml> |
| 160 <conditional name="remove_gappy_sequences_cond"> | 158 <conditional name="remove_gappy_sequences_cond"> |
| 161 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?"> | 159 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?"> |
| 162 <option value="no" selected="true">No</option> | 160 <option value="no" selected="true">No</option> |
| 163 <option value="yes">Yes</option> | 161 <option value="yes">Yes</option> |
| 164 </param> | 162 </param> |
| 165 <when value="no" /> | 163 <when value="no"> |
| 164 <expand macro="cond_multiple_sequence_alignments" /> | |
| 165 </when> | |
| 166 <when value="yes"> | 166 <when value="yes"> |
| 167 <conditional name="trim_type_cond"> | 167 <conditional name="trim_type_cond"> |
| 168 <param name="trim_type" type="select" label="Select process used for gap trimming"> | 168 <param name="trim_type" type="select" label="Select process used for gap trimming"> |
| 169 <option value="gap_trimming" selected="true">Nucleotide based </option> | 169 <option value="gap_trimming" selected="true">Nucleotide based </option> |
| 170 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option> | 170 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option> |
| 181 </param> | 181 </param> |
| 182 <when value="no" /> | 182 <when value="no" /> |
| 183 <when value="yes"> | 183 <when value="yes"> |
| 184 <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" /> | 184 <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" /> |
| 185 <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/> | 185 <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations for orthogroups realignments" help="Zero value has no affect"/> |
| 186 <expand macro="cond_multiple_sequence_alignments" /> | |
| 186 </when> | 187 </when> |
| 187 </conditional> | 188 </conditional> |
| 188 </when> | 189 </when> |
| 189 </conditional> | 190 </conditional> |
| 190 </xml> | 191 </xml> |