Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 135:08d59ab0eacb draft

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author greg
date Fri, 28 Apr 2017 13:54:18 -0400
parents 5de0658ef884
children 4fbae9f0cc6f
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134:5de0658ef884 135:08d59ab0eacb
275 * **Global selection configuration** - the upper limit values of the following two parameters vary depending on the selected gene family scaffold, and the tool will produce an error if the value exceeds the number of species in the circumscribed scaffold. 275 * **Global selection configuration** - the upper limit values of the following two parameters vary depending on the selected gene family scaffold, and the tool will produce an error if the value exceeds the number of species in the circumscribed scaffold.
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277 * **Minimum single copy taxa** - minimum number of taxa with single copy genes in the orthogroup. 277 * **Minimum single copy taxa** - minimum number of taxa with single copy genes in the orthogroup.
278 * **Minimum taxa present** - minimum number of taxa present in the orthogroup. 278 * **Minimum taxa present** - minimum number of taxa present in the orthogroup.
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280 * **Custom selection configuration** - select ‘Yes’ to enable selection of a single copy configuration file. Scaffold configuration templates (.singleCopy.config) of how to customize single/low-copy orthogroups selection can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and also available at the PlantTribes GitHub repository (https://github.com/dePamphilis/PlantTribes/config ). Single/low-copy settings shown in these templates are used as defaults if ‘No’ is selected. 280 * **Custom selection configuration** - select ‘Yes’ to enable selection of a single copy configuration file. Scaffold configuration templates (.singleCopy.config) of how to customize single/low-copy orthogroups selection can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and also available at the PlantTribes GitHub `repository`_. Single/low-copy settings shown in these templates are used as defaults if ‘No’ is selected.
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282 .. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config
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282 * **Custom selection file** - select a single/low-copy customized configuration file from your history. 284 * **Custom selection file** - select a single/low-copy customized configuration file from your history.
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284 * **Orthogroups fasta configuration** - select ‘Yes’ to create proteins orthogroups fasta files for the classified sequences. 286 * **Orthogroups fasta configuration** - select ‘Yes’ to create proteins orthogroups fasta files for the classified sequences.
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