Mercurial > repos > greg > plant_tribes_gene_family_phylogeny_builder
comparison gene_family_phylogeny_builder.xml @ 8:994e90ae9217 draft
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| author | greg |
|---|---|
| date | Wed, 06 Jun 2018 09:24:38 -0400 |
| parents | c088c185f63f |
| children | ea8cbe5a8cd0 |
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| 7:c088c185f63f | 8:994e90ae9217 |
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| 1 <tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.3.0"> | 1 <tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.3.1"> |
| 2 <description>builds phylogenetic trees of aligned orthologous gene family clusters</description> | 2 <description>builds phylogenetic trees of aligned orthologous gene family clusters</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <requirements> | 6 <requirements> |
| 75 <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" /> | 75 <param name="max_orthogroup_size" type="integer" value="100" min="4" label="Maximum orthogroup size" /> |
| 76 <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" /> | 76 <param name="min_orthogroup_size" type="integer" value="4" min="4" label="Minimum orthogroup size" /> |
| 77 </inputs> | 77 </inputs> |
| 78 <outputs> | 78 <outputs> |
| 79 <collection name="tree" type="list" label="${tool.name} (phylogenetic trees) on ${on_string}"> | 79 <collection name="tree" type="list" label="${tool.name} (phylogenetic trees) on ${on_string}"> |
| 80 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="nhx" /> | 80 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/orthogroups_tree" format="newick" /> |
| 81 </collection> | 81 </collection> |
| 82 <collection name="phylip" type="list" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}"> | 82 <collection name="phylip" type="list" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}"> |
| 83 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter> | 83 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter> |
| 84 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" /> | 84 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" /> |
| 85 </collection> | 85 </collection> |
| 91 <element name="3722.faa.aln" value="3722.faa.aln"/> | 91 <element name="3722.faa.aln" value="3722.faa.aln"/> |
| 92 </collection> | 92 </collection> |
| 93 </param> | 93 </param> |
| 94 <param name="tree_inference" value="fasttree"/> | 94 <param name="tree_inference" value="fasttree"/> |
| 95 <output_collection name="tree" type="list"> | 95 <output_collection name="tree" type="list"> |
| 96 <element name="3722.faa.aln.tree" file="3722.faa.aln.tree" ftype="nhx"/> | 96 <element name="3722.faa.aln.tree" file="3722.faa.aln.tree" ftype="newick"/> |
| 97 </output_collection> | 97 </output_collection> |
| 98 </test> | 98 </test> |
| 99 </tests> | 99 </tests> |
| 100 <help> | 100 <help> |
| 101 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary | 101 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary |