Mercurial > repos > galaxyp > data_manager_eggnog_mapper_abspath
annotate tool-data/eggnog_mapper_db_versioned.loc.sample @ 5:81a286e4c5a2 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
| author | galaxyp |
|---|---|
| date | Mon, 20 Jun 2022 12:49:22 +0000 |
| parents | fcb8bdd124f4 |
| children |
| rev | line source |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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1 #This is a sample file distributed with Galaxy that enables tools |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
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2 #to use a directory of eggnog_mapper data files. |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
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3 # |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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4 # eggnog-mapper requires the following files to be installed in the data directory: |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
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5 # https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz |
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fcb8bdd124f4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents:
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6 # http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.db.gz |
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3
b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
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7 # A complete diamond database is available from: |
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4
fcb8bdd124f4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit e45c15081260025e470d23975ef5a734d3f8fc66"
galaxyp
parents:
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8 # http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz |
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3
b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
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9 # |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
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10 # The python script download_eggnog_data.py, |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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11 # included with eggnog_mapper, can be used to download the files to the correct directory |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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12 # |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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13 # The near-equivalence of columns "value" and "db" is needed for the tests to work, |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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14 # and for the setting of --data_dir to the parent directory of eggnog.db |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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15 # The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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16 # See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
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changeset
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17 # In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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18 # value and db should be the same (in the example, both should be "thaNOG") |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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19 # |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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20 # |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
diff
changeset
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21 #db_version name path |
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b711f5b6bd44
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
galaxyp
parents:
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22 #5.0 eggnog_5.0 /path/to/directory/that/contains/eggnog.db |