Mercurial > repos > greg > assembly_post_processor
comparison assembly_post_processor.xml @ 22:9744a653d503 draft
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author | greg |
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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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133 | 133 |
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. |