comparison assembly_post_processor.xml @ 17:63a4a0f127da draft

Uploaded

16:1e639e679f61

 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble.
 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.
 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the [Data Manager PlantTribes Scaffolds Downloader tool](https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_plant_tribes_scaffolds_downloader/4c96b684f0fd).
 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
 * **Remove sites in alignments with gaps of** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.
 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.

17:63a4a0f127da

 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble.
 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.
 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the `Data Manager PlantTribes Scaffolds Downloader tool<https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_plant_tribes_scaffolds_downloader/>`_.
 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
 * **Remove sites in alignments with gaps of** - Removes gappy sites in alignments (i.e. 0.1 removes sites with 90% gaps): [0.0 to 1.0]
 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.
 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.