Mercurial > repos > iuc > amrfinderplus

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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
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7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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1 # Test data for AMRFinderPlus
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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3 ## Create `test-db`
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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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()`
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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6 2. Remove `AMR_DNA` files that are not `Enterococcus`
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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7 3. Remove lines not related to `Enterococcus` in `taxgroup.tab`
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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8 4. Keep in `AMR_CDS`, `AMRProt`, and `ReferenceGeneCatalog.txt` only sequences listed in `to_keep_from_test-db`
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents:
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9 5. Keep in `amr_targets.fa` only sequences listed in `amr_targets_to_keep_from_test-db`
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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10 6. Copy the `AMR.LIB` from a previous version
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents:
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11 7. Run the data-manager Python script after modifying `main` function like this:
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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13 ```
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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14 amrfinderplus_download.download_amrfinderplus_db()
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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15 amrfinderplus_download.amrfinderplus_db_path = f'{amrfinderplus_download._output_dir}/{amrfinderplus_download._db_name}'
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
parents:
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16 amrfinderplus_download.make_hmm_profile()
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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17 amrfinderplus_download.make_blastdb()
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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18 ```
7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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7844dbe4f8e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
iuc
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20 6. Move the `amrfinderplus-db` folder content to `test-db`