Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.xml @ 52:3adaaeb651c0 draft

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author greg
date Mon, 09 Oct 2017 08:58:39 -0400
parents 9962341547d3
children 24774c743d31
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51:9962341547d3 52:3adaaeb651c0
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100 * **Rooting order configuration** - select 'Yes' to enable selection of a rooting order configuration file for RAxML. Scaffold configuration templates (.rootingOrder.config) of how to customize the RAxML ML tree rooting order can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and is also available at the PlantTribes GitHub `repository`_. Phylogenetic tree rooting order settings shown in these templates are used as defaults if 'No' is selected. 100 * **Rooting order configuration** - select 'Yes' to enable selection of a rooting order configuration file for RAxML. Scaffold configuration templates (.rootingOrder.config) of how to customize the RAxML ML tree rooting order can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and is also available at the PlantTribes GitHub `repository`_. Phylogenetic tree rooting order settings shown in these templates are used as defaults if 'No' is selected.
101 * **Bootstrap replicates** - number of bootstrap replicates for RAxML to conduct a rapid bootstrap analysis and search for the best-scoring ML tree (default = 100). 101 * **Bootstrap replicates** - number of bootstrap replicates for RAxML to conduct a rapid bootstrap analysis and search for the best-scoring ML tree (default = 100).
102 * **Maximum orthogroup size** - maximum number of sequences allowed in orthogroup alignments (default = 100). 102 * **Maximum orthogroup size** - maximum number of sequences allowed in orthogroup alignments (default = 100).
103 * **Minimum orthogroup size** - minimum number of sequences allowed in orthogroup alignments (default = 4). 103 * **Minimum orthogroup size** - minimum number of sequences allowed in orthogroup alignments (default = 4).
104 * **Output additional directory of phylogenetic tree files** - selecting 'Yes' will produce an additional output that has an associated directory of files that are copies of the elements of the phylogenetic trees output dataset collection (this output will be used for future downstream tools).
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106 .. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config 105 .. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config
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108 </help> 107 </help>
109 <citations> 108 <citations>