Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 124:5f2d55dca8b5 draft

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author greg
date Tue, 21 Mar 2017 10:50:00 -0400
parents 5fc33b2cbccc
children 1d3d50fbf3ca
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123:5fc33b2cbccc 124:5f2d55dca8b5
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272 * **Single copy orthogroups configuration** - select ‘Yes’ to enable single/low-copy orthogroups selection configuration options. 272 * **Single copy orthogroups configuration** - select ‘Yes’ to enable single/low-copy orthogroups selection configuration options.
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274 * **Selection criterion** - single/low-copy orthogroups selection criterion. PlantTribes provides custom and global selection criteria for selecting user defined single/low-copy scaffold orthogoups. 274 * **Selection criterion** - single/low-copy orthogroups selection criterion. PlantTribes provides custom and global selection criteria for selecting user defined single/low-copy scaffold orthogoups.
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276 * **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. 276 * **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.
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278 * **Custom selection file** - select a single/low-copy customized configuration file from your history. 278 * **Custom selection file** - select a single/low-copy customized configuration file from your history.
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280 * **Global selection configuration** 280 * **Global selection configuration**
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282 * **Minimum single copy taxa** - minimum number of taxa with single copy genes in the orthogroup. 282 * **Minimum single copy taxa** - minimum number of taxa with single copy genes in the orthogroup.
283 * **Minimum taxa present** - minimum number of taxa present in the orthogroup. 283 * **Minimum taxa present** - minimum number of taxa present in the orthogroup.
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285 * **Orthogroups fasta configuration** - select ‘Yes’ to create proteins orthogroups fasta files for the classified sequences. 285 * **Orthogroups fasta configuration** - select ‘Yes’ to create proteins orthogroups fasta files for the classified sequences.
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287 * **Orthogroups coding sequences** - select ‘Yes’ to create corresponding coding sequences orthogroups fasta files for the classified protein sequences. Requires coding sequences fasta file corresponding proteins fasta file to be selected from your history. 287 * **Orthogroups coding sequences** - select ‘Yes’ to create corresponding coding sequences orthogroups fasta files for the classified protein sequences. Requires coding sequences fasta file corresponding to the proteins fasta file to be selected from your history.
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289 * **Coding sequences fasta file** - select coding sequences fasta file corresponding to the proteins fasta file from your history. 289 * **Coding sequences fasta file** - select coding sequences fasta file corresponding to the proteins fasta file from your history.
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291 </help> 291 </help>
292 <citations> 292 <citations>