Mercurial > repos > iuc > amrfinderplus

diff 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
date: Thu, 30 May 2024 13:07:03 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/README.md	Thu May 30 13:07:03 2024 +0000
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+# Test data for AMRFinderPlus
+
+## Create `test-db` 
+
+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()`
+2. Remove `AMR_DNA` files that are not `Enterococcus`
+3. Remove lines not related to `Enterococcus` in `taxgroup.tab`
+4. Keep in `AMR_CDS`, `AMRProt`, and `ReferenceGeneCatalog.txt` only sequences listed in `to_keep_from_test-db`
+5. Keep in `amr_targets.fa` only sequences listed in `amr_targets_to_keep_from_test-db`
+6. Copy the `AMR.LIB` from a previous version
+7. Run the data-manager Python script after modifying `main` function like this:
+
+    ```
+    amrfinderplus_download.download_amrfinderplus_db()
+    amrfinderplus_download.amrfinderplus_db_path = f'{amrfinderplus_download._output_dir}/{amrfinderplus_download._db_name}'
+    amrfinderplus_download.make_hmm_profile()
+    amrfinderplus_download.make_blastdb()
+    ```
+
+6. Move the `amrfinderplus-db` folder content to `test-db`
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