Mercurial > repos > greg > assembly_post_processor
changeset 17:63a4a0f127da draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 13 Feb 2017 07:46:00 -0500 |
| parents | 1e639e679f61 |
| children | 16c5477b3cb3 |
| files | assembly_post_processor.xml |
| diffstat | 1 files changed, 1 insertions(+), 1 deletions(-) [+] |
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--- a/assembly_post_processor.xml Mon Feb 13 07:40:02 2017 -0500 +++ b/assembly_post_processor.xml Mon Feb 13 07:46:00 2017 -0500 @@ -136,7 +136,7 @@ * **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). + * **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.