Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 19:dbad8b1486fb draft

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author greg
date Mon, 13 Feb 2017 07:48:41 -0500
parents 16c5477b3cb3
children 37abc8473df1
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18:16c5477b3cb3 19:dbad8b1486fb
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135 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder. 135 * **Prediction method for coding regions** - The prediction method for coding regions; one of ESTScan or TransDecoder.
136 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms. 136 * **Scores matrices** - Scores matrices that reflect the codons preferences in the studied organisms.
137 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble. 137 * **Target gene family assembly?** - Select 'Yes' to target gene families to assemble.
138 * **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 * **List of orthogroup identifiers for target gene families to assemble** - History item with a list of orthogroup identifiers for target gene families to assemble.
139 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the `Data Manager PlantTribes Scaffolds Downloader tool 139 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the Data Manager PlantTribes Scaffolds Downloader tool".
140 <https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_plant_tribes_scaffolds_downloader/>`_.
141 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). 140 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
142 * **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 * **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]
143 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library. 142 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.
144 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions. 143 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
145 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions. 144 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.