Mercurial > repos > galaxyp > data_manager_eggnog_mapper

annotate data_manager/data_manager_eggnog.xml @ 1:077cf0a99144 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
author galaxyp
date Fri, 04 Sep 2020 21:38:59 +0000
parents 6d8144eef202
children 3d82020b1e3b
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077cf0a99144 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
galaxyp
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1 <tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@" tool_type="manage_data">
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6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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2 <description>eggnog data</description>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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3 <macros>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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4 <import>eggnog_macros.xml</import>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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5 </macros>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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6 <expand macro="requirements"/>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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7 <expand macro="version_command"/>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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8 <command detect_errors="exit_code"><![CDATA[
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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9 #import json, os
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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10 #set params = json.loads(open(str($out_file)).read())
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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11 #set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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12 @DOWNLOAD_CMD@
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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13 ]]></command>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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14 <inputs>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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15 <expand macro="data_manager_params"/>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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16 </inputs>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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17 <expand macro="data_manager_outputs"/>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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18 <tests>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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19 <expand macro="data_manager_test"/>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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20 </tests>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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21 <help><![CDATA[
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077cf0a99144 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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22 This tool downloads eggnog data using download_eggnog_data.py
077cf0a99144 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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23 and populates the data tables: eggnog_mapper_db.
077cf0a99144 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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24 The data is located at: http://eggnog5.embl.de/download/emapperdb-5.0.0/
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6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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25 can vary from 1G to 80G in size.
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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26
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077cf0a99144 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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27 This will install data relative to the galaxy_data_manager_data_path declared in config/galaxy.yml
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6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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28 in directory eggnog_data/<eggnog data version>/.
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077cf0a99144 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 2200885b5049b2d952959001c8a9b5ae5c62bee5"
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29 The eggnog version is queried from the downloaded SQlite eggnog.db from table version.
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6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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30 ]]></help>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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31 <expand macro="citations"/>
6d8144eef202 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit ba81f4bfe31157aa6b986e81d5e4405ae1372b3b"
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32 </tool>