Mercurial > repos > greg > phylogenomics_analysis
comparison macros.xml @ 75:063a39e39705 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 22 Mar 2017 11:29:09 -0400 |
| parents | 7170b072b40a |
| children | 36b7c987177d |
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| 74:7170b072b40a | 75:063a39e39705 |
|---|---|
| 53 </when> | 53 </when> |
| 54 </conditional> | 54 </conditional> |
| 55 </when> | 55 </when> |
| 56 </conditional> | 56 </conditional> |
| 57 </xml> | 57 </xml> |
| 58 <xml name="cond_phylogenomic_trees_start"> | 58 <xml name="cond_phylogenomic_trees_ptortho"> |
| 59 <conditional name="phylogenetic_trees_cond"> | 59 <conditional name="phylogenetic_trees_cond"> |
| 60 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?"> | 60 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?"> |
| 61 <option value="no" selected="true">No</option> | 61 <option value="no" selected="true">No</option> |
| 62 <option value="yes">Yes</option> | 62 <option value="yes">Yes</option> |
| 63 </param> | 63 </param> |
| 83 </when> | 83 </when> |
| 84 <when value="fasttree" /> | 84 <when value="fasttree" /> |
| 85 </conditional> | 85 </conditional> |
| 86 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" /> | 86 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" /> |
| 87 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" /> | 87 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" /> |
| 88 </xml> | 88 </when> |
| 89 <xml name="param_sequence_type"> | 89 </conditional> |
| 90 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)"> | 90 </xml> |
| 91 <option value="protein" selected="true">Amino acid based</option> | 91 <xml name="cond_phylogenomic_trees_ptorthocs"> |
| 92 <option value="dna">Nucleotide based</option> | 92 <conditional name="phylogenetic_trees_cond"> |
| 93 </param> | 93 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?"> |
| 94 </xml> | 94 <option value="no" selected="true">No</option> |
| 95 <xml name="cond_phylogenomic_trees_end"> | 95 <option value="yes">Yes</option> |
| 96 </param> | |
| 97 <when value="no" /> | |
| 98 <when value="yes"> | |
| 99 <conditional name="tree_inference_cond"> | |
| 100 <param name="tree_inference" type="select" label="Phylogenetic trees inference method"> | |
| 101 <option value="raxml" selected="true">RAxML</option> | |
| 102 <option value="fasttree">FastTree</option> | |
| 103 </param> | |
| 104 <when value="raxml"> | |
| 105 <conditional name="rooting_order_file_cond"> | |
| 106 <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup"> | |
| 107 <option value="no" selected="true">No</option> | |
| 108 <option value="yes">Yes</option> | |
| 109 </param> | |
| 110 <when value="no" /> | |
| 111 <when value="yes"> | |
| 112 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" /> | |
| 113 </when> | |
| 114 </conditional> | |
| 115 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" /> | |
| 116 </when> | |
| 117 <when value="fasttree" /> | |
| 118 </conditional> | |
| 119 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" /> | |
| 120 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" /> | |
| 121 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)"> | |
| 122 <option value="protein" selected="true">Amino acid based</option> | |
| 123 <option value="dna">Nucleotide based</option> | |
| 124 </param> | |
| 96 </when> | 125 </when> |
| 97 </conditional> | 126 </conditional> |
| 98 </xml> | 127 </xml> |
| 99 <xml name="cond_remove_gappy_sequences"> | 128 <xml name="cond_remove_gappy_sequences"> |
| 100 <conditional name="remove_gappy_sequences_cond"> | 129 <conditional name="remove_gappy_sequences_cond"> |