Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 122:78d2a8b63c13 draft

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author greg
date Tue, 21 Mar 2017 10:38:28 -0400
parents cf5a7194d866
children 5fc33b2cbccc
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121:cf5a7194d866 122:78d2a8b63c13
259 **Required options** 259 **Required options**
260 260
261 * **Proteins fasta file** - proteins fasta file either produced by the AssemblyPostProcessor tool or an external source selected from your history. 261 * **Proteins fasta file** - proteins fasta file either produced by the AssemblyPostProcessor tool or an external source selected from your history.
262 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds [2-4] installed into Galaxy by the PlantTribes Scaffold Data Manager tool. 262 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds [2-4] installed into Galaxy by the PlantTribes Scaffold Data Manager tool.
263 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool. 263 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
264 * **Protein classifier** - Classifier to assign protein sequences into a specified scaffold orthogroups. PlantTribes implements three classification approaches; blastp (faster)[5], hmmscan (slower but more sensitive to the remote homologs)[6], and both blastp and hmmscan (more exhaustive). 264 * **Protein classifier** - classifier to assign protein sequences into a specified scaffold orthogroups. PlantTribes implements three classification approaches; blastp (faster)[5], hmmscan (slower but more sensitive to the remote homologs)[6], and both blastp and hmmscan (more exhaustive).
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266 **Other options** 266 **Other options**
267 267
268 * **Super orthogroups configuration** - select ‘Yes’ to enable super orthogroups configuration options. Super orthogroups are constructed through a second iteration of MCL clustering to connect distant, but potentially related orthogroup clusters. 268 * **Super orthogroups configuration** - select ‘Yes’ to enable super orthogroups configuration options. Super orthogroups are constructed through a second iteration of MCL clustering to connect distant, but potentially related orthogroup clusters.
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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** - Used with "Global selection" configuration only. 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 proteins fasta file to be selected from your history.
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