Mercurial > repos > iuc > amrfinderplus
comparison test-data/README.md @ 7:7844dbe4f8e2 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
| author | iuc |
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| date | Thu, 30 May 2024 13:07:03 +0000 |
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| 6:1920244e2895 | 7:7844dbe4f8e2 |
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| 1 # Test data for AMRFinderPlus | |
| 2 | |
| 3 ## Create `test-db` | |
| 4 | |
| 5 1. Download ARMFinderPlus database from NCBI using the data-manager Python script after modifying the `main` function to keep only `amrfinderplus_download.download_amrfinderplus_db()` | |
| 6 2. Remove `AMR_DNA` files that are not `Enterococcus` | |
| 7 3. Remove lines not related to `Enterococcus` in `taxgroup.tab` | |
| 8 4. Keep in `AMR_CDS`, `AMRProt`, and `ReferenceGeneCatalog.txt` only sequences listed in `to_keep_from_test-db` | |
| 9 5. Keep in `amr_targets.fa` only sequences listed in `amr_targets_to_keep_from_test-db` | |
| 10 6. Copy the `AMR.LIB` from a previous version | |
| 11 7. Run the data-manager Python script after modifying `main` function like this: | |
| 12 | |
| 13 ``` | |
| 14 amrfinderplus_download.download_amrfinderplus_db() | |
| 15 amrfinderplus_download.amrfinderplus_db_path = f'{amrfinderplus_download._output_dir}/{amrfinderplus_download._db_name}' | |
| 16 amrfinderplus_download.make_hmm_profile() | |
| 17 amrfinderplus_download.make_blastdb() | |
| 18 ``` | |
| 19 | |
| 20 6. Move the `amrfinderplus-db` folder content to `test-db` |