Workflow Type: Galaxy
Open
This workflow begins from a set of genome assemblies of different samples, strains, species. The genome is first annotated with Funnanotate. Predicted proteins are furtner annotated with Busco. Next, 'ProteinOrtho' finds orthologs across the samples and makes orthogroups. Orthogroups where all samples are represented are extracted. Orthologs in each orthogroup are aligned with ClustalW. Test dataset: https://zenodo.org/record/6610704#.Ypn3FzlBw5k
Inputs
ID | Name | Description | Type |
---|---|---|---|
Input genomes as collection | Input genomes as collection | n/a | n/a |
evidences | evidences | runtime parameter for tool Funannotate predict annotation | n/a |
evidences | evidences | runtime parameter for tool Funannotate predict annotation | n/a |
genemark | genemark | runtime parameter for tool Funannotate predict annotation | n/a |
genemark | genemark | runtime parameter for tool Funannotate predict annotation | n/a |
other_predictors | other_predictors | runtime parameter for tool Funannotate predict annotation | n/a |
other_predictors | other_predictors | runtime parameter for tool Funannotate predict annotation | n/a |
other_predictors | other_predictors | runtime parameter for tool Funannotate predict annotation | n/a |
other_predictors | other_predictors | runtime parameter for tool Funannotate predict annotation | n/a |
parameters | parameters | runtime parameter for tool Funannotate predict annotation | n/a |
Steps
ID | Name | Description |
---|---|---|
0 | Input genomes as collection | |
1 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 |
2 | RepeatMasker | toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0 |
3 | Funannotate predict annotation | toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2 |
4 | Extract ORF | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02 |
5 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1 |
6 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
7 | Proteinortho | toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1 |
8 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4 |
9 | Filter | Filter1 |
10 | Proteinortho grab proteins | toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1 |
11 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1 |
12 | ClustalW | toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
outfile | outfile | n/a | |
output_masked_genome | output_masked_genome | n/a | |
output_log | output_log | n/a | |
output_table | output_table | n/a | |
output_repeat_catalog | output_repeat_catalog | n/a | |
annot_gbk | annot_gbk | n/a | |
aa_output | aa_output | n/a | |
nc_output | nc_output | n/a | |
out_file1 | out_file1 | n/a | |
output | output | n/a | |
blastgraph | blastgraph | n/a | |
proteinortho | proteinortho | n/a | |
proteinorthograph | proteinorthograph | n/a | |
busco_sum | busco_sum | n/a | |
busco_table | busco_table | n/a | |
busco_missing | busco_missing | n/a | |
out_file1 | out_file1 | n/a | |
listproteinorthograbproteins | listproteinorthograbproteins | n/a | |
out_file1 | out_file1 | n/a | |
output | output | n/a | |
dnd | dnd | n/a |
Version History
Version 1 (earliest) Created 6th Jun 2022 at 15:05 by Miguel Roncoroni
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Miguel Roncoroni
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Created: 6th Jun 2022 at 15:05
Last used: 29th Jun 2022 at 03:45

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