Mercurial > repos > jjohnson > data_manager_eggnog_mapper_abspath

annotate data_manager/data_manager_eggnog.xml @ 0:d4e2e8176db8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
author jjohnson
date Thu, 07 Nov 2019 12:42:32 -0500
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d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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1 <tool id="data_manager_eggnog_abspath" name="EggNOG DB Download" version="@VERSION@.0" tool_type="manage_data">
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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2 <description>eggnog data to a specified directory</description>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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3 <macros>
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jjohnson
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4 <import>eggnog_macros.xml</import>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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5 </macros>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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6 <expand macro="requirements"/>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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7 <expand macro="version_command"/>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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8 <command detect_errors="exit_code"><![CDATA[
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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9 #set $install_path = $target_path
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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10 @DOWNLOAD_CMD@
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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11 ]]></command>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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12 <inputs>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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13 <param name="target_path" type="text" value="" label="Download Destination"
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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14 help="Full path to where the eggnod data should be installed.">
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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15 <validator type="regex" message="Must be an absolute path">^/.*$</validator>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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16 </param>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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17 <expand macro="data_manager_params"/>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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18 </inputs>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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19 <expand macro="data_manager_outputs"/>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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20 <tests>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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21 <expand macro="data_manager_test"/>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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22 </tests>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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23 <help><![CDATA[
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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24 This tool downloads eggnog data using download_eggnog_data.py
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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25 and populates the data tables: eggnog_mapper_db and eggnog_mapper_hmm_dbs.
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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26 The data is located at: http://eggnogdb.embl.de/download/emapperdb-4.5.1/
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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27 The optional eggNOG HMM databases: http://eggnogdb.embl.de/download/emapperdb-4.5.1/hmmdb_levels/
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
jjohnson
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28 can vary from 1G to 80G in size.
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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29
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30 The data will be downloaded to the specified directory. This allows adding hmmdb_levels to an existing download.
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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31 You should not mix eggnog data versions in the same directory.
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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32 ]]></help>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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33 <expand macro="citations"/>
d4e2e8176db8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/data_manager_eggnog_mapper_abspath commit 4ac0d4d79233ac5151ab32741183adbfecb70a45
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34 </tool>