Mercurial > repos > jjohnson > data_manager_eggnog_mapper
annotate data_manager/data_manager_eggnog.xml @ 1:df699325bb3b draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 288c3043b10594647e9f6e5de56bf98a38779f75-dirty
author | jjohnson |
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date | Fri, 08 Nov 2019 14:32:49 -0500 |
parents | 6abbdf623176 |
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6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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1 <tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@.1" tool_type="manage_data"> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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2 <description>eggnog data</description> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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3 <macros> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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4 <import>eggnog_macros.xml</import> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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5 </macros> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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6 <expand macro="requirements"/> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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7 <expand macro="version_command"/> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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8 <command detect_errors="exit_code"><![CDATA[ |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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9 #import json, os |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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10 #set params = json.loads(open(str($out_file)).read()) |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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11 #set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace') |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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12 @DOWNLOAD_CMD@ |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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13 ]]></command> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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14 <inputs> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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15 <expand macro="data_manager_params"/> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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16 </inputs> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
diff
changeset
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17 <expand macro="data_manager_outputs"/> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
diff
changeset
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18 <tests> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
diff
changeset
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19 <expand macro="data_manager_test"/> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
diff
changeset
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20 </tests> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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21 <help><![CDATA[ |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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22 This tool downloads eggnog data using download_eggnog_data.py |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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23 and populates the data tables: eggnog_mapper_db and eggnog_mapper_hmm_dbs. |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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24 The data is located at: http://eggnogdb.embl.de/download/emapperdb-4.5.1/ |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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25 The optional eggNOG HMM databases: http://eggnogdb.embl.de/download/emapperdb-4.5.1/hmmdb_levels/ |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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26 can vary from 1G to 80G in size. |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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27 |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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28 This will install data relative to the galaxy_data_manager_data_path declared in config/galaxy.yml |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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29 in directory eggnog_data/<eggnog data version>/. |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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30 The eggnog version is queried from the downloaded SQlite eggnog.db from table version. |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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31 ]]></help> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
parents:
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32 <expand macro="citations"/> |
6abbdf623176
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit c4fb2c42cd1f2ce8748a2d949238eea70635f11b-dirty
jjohnson
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33 </tool> |