annotate data_manager/data_manager_eggnog.xml @ 4:516eb4e1cf8e draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
author galaxyp
date Mon, 20 Jun 2022 12:48:56 +0000
parents 5a2ffc486246
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516eb4e1cf8e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit 75035b2919ce95fa8d3b785d86c7c7c9da531db2
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1 <tool id="data_manager_eggnog" name="EggNOG DB Download" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="18.09">
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2 <description>eggnog data</description>
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3 <macros>
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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>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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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())
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3d82020b1e3b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
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11 #set install_path = $params['output_data'][0]['extra_files_path']
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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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12 @DOWNLOAD_CMD@
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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>
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15 <expand macro="data_manager_params"/>
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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"/>
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18 <tests>
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19 <expand macro="data_manager_test"/>
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20 </tests>
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21 <help><![CDATA[
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22 This tool downloads eggnog data using download_eggnog_data.py
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23 and populates the data tables: eggnog_mapper_db_versioned.
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5a2ffc486246 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit e45c15081260025e470d23975ef5a734d3f8fc66"
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24 The data is located at: http://eggnog5.embl.de/download/emapperdb-5.0.2/
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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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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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29 The eggnog version is queried from the downloaded SQlite eggnog.db from table version.
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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"/>
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32 </tool>