Mercurial > repos > galaxyp > data_manager_eggnog_mapper
changeset 2:3d82020b1e3b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper/eggnog_mapper_data_manager commit fd234f7532b34a1b6ced0d3ac53a8f42348e23f7"
| author | galaxyp |
|---|---|
| date | Fri, 19 Feb 2021 18:53:40 +0000 |
| parents | 077cf0a99144 |
| children | 5a2ffc486246 |
| files | data_manager/data_manager_eggnog.py data_manager/data_manager_eggnog.xml data_manager/eggnog_macros.xml data_manager_conf.xml test-data/cached_locally/eggnog_mapper_db.loc test-data/cached_locally/eggnog_mapper_db_versioned.loc tool-data/eggnog_mapper_db.loc.sample tool-data/eggnog_mapper_db_versioned.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| diffstat | 10 files changed, 53 insertions(+), 38 deletions(-) [+] |
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--- a/data_manager/data_manager_eggnog.py Fri Sep 04 21:38:59 2020 +0000 +++ b/data_manager/data_manager_eggnog.py Fri Feb 19 18:53:40 2021 +0000 @@ -39,11 +39,18 @@ # params = json.loads(open(args.config_file).read()) dm_dict = {} dm_dict['data_tables'] = dm_dict.get('data_tables', {}) - data_table = 'eggnog_mapper_db' + data_table = 'eggnog_mapper_db_versioned' dm_dict['data_tables'][data_table]\ = dm_dict['data_tables'].get(data_table, []) + # Versionning is super confusing: + # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5) + # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0) + # db v4.5 are not compatible with eggnog-mapper 2.0 + version = "2.0" + if "4.5" in db_version: + version = "1.0" data_table_entry = dict(value=db_version, name=db_version, - path=args.install_path) + path=args.install_path, version=version) dm_dict['data_tables'][data_table].append(data_table_entry) # save info to json file
--- a/data_manager/data_manager_eggnog.xml Fri Sep 04 21:38:59 2020 +0000 +++ b/data_manager/data_manager_eggnog.xml Fri Feb 19 18:53:40 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@" tool_type="manage_data"> +<tool id="data_manager_eggnog" name="EggNOG DB Download" version="@VERSION@+galaxy1" tool_type="manage_data" profile="18.09"> <description>eggnog data</description> <macros> <import>eggnog_macros.xml</import> @@ -8,7 +8,7 @@ <command detect_errors="exit_code"><![CDATA[ #import json, os #set params = json.loads(open(str($out_file)).read()) -#set install_path = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace') +#set install_path = $params['output_data'][0]['extra_files_path'] @DOWNLOAD_CMD@ ]]></command> <inputs> @@ -20,7 +20,7 @@ </tests> <help><![CDATA[ This tool downloads eggnog data using download_eggnog_data.py -and populates the data tables: eggnog_mapper_db. +and populates the data tables: eggnog_mapper_db_versioned. The data is located at: http://eggnog5.embl.de/download/emapperdb-5.0.0/ can vary from 1G to 80G in size.
--- a/data_manager/eggnog_macros.xml Fri Sep 04 21:38:59 2020 +0000 +++ b/data_manager/eggnog_macros.xml Fri Feb 19 18:53:40 2021 +0000 @@ -1,7 +1,14 @@ <?xml version="1.0"?> <macros> <token name="@VERSION@">2.0.1</token> - <token name="@EGGNOG_DB_VERSION@">5.0</token> + <token name="@EGGNOG_DB_VERSION@">2.0</token> + <!-- + # Versionning is super confusing: + # eggnog-mapper 1.* needed a db v4.5 (based on eggnog v4.5) + # eggnog-mapper 2.0 needs a db v2.0 (based on eggnog v5.0) + # db v4.5 are not compatible with eggnog-mapper 2.0 + --> + <token name="@IDX_VERSION@">2.0</token> <xml name="citations"> <citations> <citation type="doi">10.1093/nar/gkv1248</citation> @@ -47,7 +54,7 @@ <yield /> <output name="out_file"> <assert_contents> - <has_text text="eggnog_mapper_db" /> + <has_text text="eggnog_mapper_db_versioned" /> <has_text text="@EGGNOG_DB_VERSION@" /> </assert_contents> </output>
--- a/data_manager_conf.xml Fri Sep 04 21:38:59 2020 +0000 +++ b/data_manager_conf.xml Fri Feb 19 18:53:40 2021 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <data_managers> <data_manager tool_file="data_manager/data_manager_eggnog.xml" id="data_manager_eggnog" > - <data_table name="eggnog_mapper_db"> <!-- Defines a Data Table to be modified. --> + <data_table name="eggnog_mapper_db_versioned"> <!-- Defines a Data Table to be modified. --> <output> <!-- Handle the output of the Data Manager Tool --> <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool --> <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool --> @@ -12,6 +12,7 @@ <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/eggnog_data/${value}</value_translation> <value_translation type="function">abspath</value_translation> </column> + <column name="version" /> </output> </data_table> </data_manager>
--- a/test-data/cached_locally/eggnog_mapper_db.loc Fri Sep 04 21:38:59 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -#value name path -5.0 eggNOG_5.0 ${__HERE__}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/eggnog_mapper_db_versioned.loc Fri Feb 19 18:53:40 2021 +0000 @@ -0,0 +1,2 @@ +#value name path version +2.0 eggNOG_2.0 ${__HERE__} 2.0
--- a/tool-data/eggnog_mapper_db.loc.sample Fri Sep 04 21:38:59 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of eggnog_mapper data files. -# -# eggnog-mapper requires the following files to be installed in the data directory: -# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz -# http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz -# A complete diamond database is available from: -# http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog_proteins.dmnd.gz -# -# The python script download_eggnog_data.py, -# included with eggnog_mapper, can be used to download the files to the correct directory -# -# The near-equivalence of columns "value" and "db" is needed for the tests to work, -# and for the setting of --data_dir to the parent directory of eggnog.db -# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. -# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases -# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, -# value and db should be the same (in the example, both should be "thaNOG") -# -# -#db_version name path -#5.0 eggnog_5.0 /path/to/directory/that/contains/eggnog.db
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/eggnog_mapper_db_versioned.loc.sample Fri Feb 19 18:53:40 2021 +0000 @@ -0,0 +1,22 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of eggnog_mapper data files. +# +# eggnog-mapper requires the following files to be installed in the data directory: +# https://github.com/jhcepas/eggnog-mapper/blob/master/data/og2level.tsv.gz +# http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog.db.gz +# A complete diamond database is available from: +# http://eggnog5.embl.de/download/emapperdb-5.0.0/eggnog_proteins.dmnd.gz +# +# The python script download_eggnog_data.py, +# included with eggnog_mapper, can be used to download the files to the correct directory +# +# The near-equivalence of columns "value" and "db" is needed for the tests to work, +# and for the setting of --data_dir to the parent directory of eggnog.db +# The complicated eggNOG database structure makes passing custom HMM databases somewhat tricky. +# See test-data/cached_locally/eggnog_mapper.loc for how this was done with the included test databases +# In all other cases, when the appropriate HMM database (for example, "thaNOG") was downloaded from eggnogdb.embl.de, +# value and db should be the same (in the example, both should be "thaNOG") +# +# +#db_version name path +#5.0 eggnog_5.0 /path/to/directory/that/contains/eggnog.db
--- a/tool_data_table_conf.xml.sample Fri Sep 04 21:38:59 2020 +0000 +++ b/tool_data_table_conf.xml.sample Fri Feb 19 18:53:40 2021 +0000 @@ -1,7 +1,7 @@ <tables> <!-- Locations of all eggnog_mapper data --> - <table name="eggnog_mapper_db" comment_char="#" allow_duplicate_entries="False"> - <columns>value,name,path</columns> - <file path="tool-data/eggnog_mapper_db.loc" /> + <table name="eggnog_mapper_db_versioned" comment_char="#" allow_duplicate_entries="False"> + <columns>value,name,path,version</columns> + <file path="tool-data/eggnog_mapper_db_versioned.loc" /> </table> </tables>
--- a/tool_data_table_conf.xml.test Fri Sep 04 21:38:59 2020 +0000 +++ b/tool_data_table_conf.xml.test Fri Feb 19 18:53:40 2021 +0000 @@ -1,7 +1,7 @@ <tables> <!-- Locations of all eggnog_mapper data --> - <table name="eggnog_mapper_db" comment_char="#"> - <columns>value,name,path</columns> - <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_db.loc" /> + <table name="eggnog_mapper_db_versioned" comment_char="#" allow_duplicate_entries="False"> + <columns>value,name,path,version</columns> + <file path="${__HERE__}/test-data/cached_locally/eggnog_mapper_db_versioned.loc" /> </table> </tables>