Mercurial > repos > greg > assembly_post_processor

comparison assembly_post_processor.xml @ 21:913c3e0354cc draft

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author greg
date Mon, 13 Feb 2017 07:59:49 -0500
parents 37abc8473df1
children 9744a653d503
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20:37abc8473df1 21:913c3e0354cc
20 #if str($prediction_method_cond.prediction_method) == 'estscan': 20 #if str($prediction_method_cond.prediction_method) == 'estscan':
21 --score_matrices '$score_matrices' 21 --score_matrices '$score_matrices'
22 #end if 22 #end if
23 #if str($options_type.options_type_selector) == 'advanced': 23 #if str($options_type.options_type_selector) == 'advanced':
24 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': 24 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
25 #set scaffold = $options_type.target_gene_family_assembly_cond.scaffold.fields.path
26 --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups' 25 --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
27 --scaffold '$scaffold' 26 --scaffold '$options_type.target_gene_family_assembly_cond.scaffold.fields.path'
28 --method '$options_type.target_gene_family_assembly_cond.method' 27 --method '$options_type.target_gene_family_assembly_cond.method'
29 #end if 28 #end if
30 --gap_trimming $options_type.gap_trimming 29 --gap_trimming $options_type.gap_trimming
31 #if str($options_type.strand_specific) == 'yes': 30 #if str($options_type.strand_specific) == 'yes':
32 --strand_specific 31 --strand_specific
134 133
135 * **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.
136 * **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.
137 * **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.
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. 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.
139 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data which is installed into Galaxy by the Data Manager PlantTribes Scaffolds Downloader tool. 138 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data, installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool.
140 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). 139 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
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] 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]
142 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library. 141 * **De novo transcriptome assembly was performed with strand-specific library?** - Select 'Yes' if de novo transcriptome assembly was performed with strand-specific library.
143 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions. 142 * **Remove repeated sequences in predicted coding regions?** - Select yes to remove repeated sequences in predicted coding regions.
144 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions. 143 * **Minimum sequence length of predicted coding regions** - Set the minimum sequence length of predicted coding regions.