comparison assembly_post_processor.xml @ 22:9744a653d503 draft

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author greg
date Mon, 13 Feb 2017 08:07:04 -0500
parents 913c3e0354cc
children fa95f44f2e1a
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21:913c3e0354cc 22:9744a653d503
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134 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder. 134 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
135 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms. 135 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
136 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble. 136 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble.
137 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble. 137 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.
138 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data, installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool.
139 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). 138 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
140 * **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] 139 * **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]
141 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library. 140 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.
142 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions. 141 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
143 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions. 142 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.