Mercurial > repos > iuc > data_manager_metaphlan_database_downloader
changeset 2:5fe20c915fa6 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
author | iuc |
---|---|
date | Tue, 28 Mar 2023 18:54:12 +0000 |
parents | 9c43baa60906 |
children | 4ba60cb14cb0 |
files | data_manager/data_manager_metaphlan_download.py data_manager/data_manager_metaphlan_download.xml data_manager_conf.xml test-data/metaphlan_database.loc test-data/metaphlan_database_versioned.loc tool-data/metaphlan_database.loc.sample tool-data/metaphlan_database_versioned.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
diffstat | 9 files changed, 43 insertions(+), 38 deletions(-) [+] |
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--- a/data_manager/data_manager_metaphlan_download.py Wed Apr 21 21:37:49 2021 +0000 +++ b/data_manager/data_manager_metaphlan_download.py Tue Mar 28 18:54:12 2023 +0000 @@ -106,7 +106,8 @@ dbkey=index, value='%s-%s' % (index, date.today().strftime("%d%m%Y")), name="MetaPhlAn clade-specific marker genes (%s)" % index, - path=str(db_dp))) + path=str(db_dp), + db_version='SGB' if 'SGB' in index else 'legacy')) if __name__ == "__main__": @@ -129,14 +130,14 @@ # Set up data tables dictionary data_tables = create_data_tables_dict() - add_data_table(data_tables, "metaphlan_database") + add_data_table(data_tables, "metaphlan_database_versioned") # Fetch data from specified data sources print("Download and build database") download_metaphlan_db( data_tables, args.index, - "metaphlan_database", + "metaphlan_database_versioned", target_dp) # Write output JSON
--- a/data_manager/data_manager_metaphlan_download.xml Wed Apr 21 21:37:49 2021 +0000 +++ b/data_manager/data_manager_metaphlan_download.xml Tue Mar 28 18:54:12 2023 +0000 @@ -1,15 +1,15 @@ -<tool id="data_manager_metaphlan_download" name="Download and build MetaPhlAn database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01"> +<tool id="data_manager_metaphlan_download" name="Download and build MetaPhlAn database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05"> <description></description> <requirements> <requirement type="package" version="@TOOL_VERSION@">metaphlan</requirement> </requirements> <macros> - <token name="@TOOL_VERSION@">3.0.7</token> + <token name="@TOOL_VERSION@">4.0.6</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <stdio> - <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> - <exit_code range="1:" level="fatal" description="Error" /> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file"/> + <exit_code range="1:" level="fatal" description="Error"/> </stdio> <command><![CDATA[ python '$__tool_directory__/data_manager_metaphlan_download.py' @@ -18,22 +18,25 @@ ]]></command> <inputs> <param name="index" type="select" label="Version"> - <option value="mpa_v30_CHOCOPhlAn_201901" selected="true">mpa_v30_CHOCOPhlAn_201901</option> + <option value="mpa_vOct22_CHOCOPhlAnSGB_202212" selected="true">mpa_vOct22_CHOCOPhlAnSGB_202212</option> + <option value="mpa_vJan21_CHOCOPhlAnSGB_202103">mpa_vJan21_CHOCOPhlAnSGB_202103</option> </param> </inputs> <outputs> <data name="out_file" format="data_manager_json" label="${tool.name}"/> </outputs> <tests> - <test expect_num_outputs="1"> - <param name="index" value="mpa_v30_CHOCOPhlAn_201901"/> - <output name="out_file"> - <assert_contents> - <has_text text="mpa_v30_CHOCOPhlAn_201901-"/> - <has_text text="MetaPhlAn clade-specific marker genes (mpa_v30_CHOCOPhlAn_201901)"/> - </assert_contents> - </output> - </test> + <!-- + <test expect_num_outputs="1"> + <param name="index" value="mpa_vOct22_CHOCOPhlAnSGB_202212"/> + <output name="out_file"> + <assert_contents> + <has_text text="mpa_vOct22_CHOCOPhlAnSGB_202212"/> + <has_text text="MetaPhlAn clade-specific marker genes (mpa_vOct22_CHOCOPhlAnSGB_202212)"/> + </assert_contents> + </output> + </test> + --> </tests> <help><![CDATA[ This tool downloads and builds the MetaPhlAn databases.
--- a/data_manager_conf.xml Wed Apr 21 21:37:49 2021 +0000 +++ b/data_manager_conf.xml Tue Mar 28 18:54:12 2023 +0000 @@ -1,12 +1,12 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager/data_manager_metaphlan_download.xml" id="data_manager_metaphlan_download" > - <data_table name="metaphlan_database"> <!-- Defines a Data Table to be modified. --> + <data_manager tool_file="data_manager/data_manager_metaphlan_download.xml" id="data_manager_metaphlan_download"> + <data_table name="metaphlan_database_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 --> - <column name="dbkey" /> <!-- columns that are going to be specified by the Data Manager Tool --> - <column name="path" output_ref="out_file" > + <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 --> + <column name="dbkey"/> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="path" output_ref="out_file"> <move type="directory"> <source>${path}</source> <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">metaphlan/data/${dbkey}</target> @@ -14,6 +14,7 @@ <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/metaphlan/data/${dbkey}</value_translation> <value_translation type="function">abspath</value_translation> </column> + <column name="db_version"/> <!-- columns that are going to be specified by the Data Manager Tool --> </output> </data_table> </data_manager>
--- a/test-data/metaphlan_database.loc Wed Apr 21 21:37:49 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of metagenomics files. -#file has this format (white space characters are TAB characters) -mpa_v30_CHOCOPhlAn_201901-20210420 MetaPhlAn clade-specific marker genes (mpa_v30_CHOCOPhlAn_201901) mpa_v30_CHOCOPhlAn_201901 /path/to/data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metaphlan_database_versioned.loc Tue Mar 28 18:54:12 2023 +0000 @@ -0,0 +1,4 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +#mpa_v30_CHOCOPhlAn_201901-20210420 MetaPhlAn clade-specific marker genes (mpa_v30_CHOCOPhlAn_201901) mpa_v30_CHOCOPhlAn_201901 /path/to/data SGB_or_legacy
--- a/tool-data/metaphlan_database.loc.sample Wed Apr 21 21:37:49 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of metagenomics files. -#file has this format (white space characters are TAB characters) -#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/metaphlan_database_versioned.loc.sample Tue Mar 28 18:54:12 2023 +0000 @@ -0,0 +1,4 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of metagenomics files. +#file has this format (white space characters are TAB characters) +#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data SGB_or_legacy
--- a/tool_data_table_conf.xml.sample Wed Apr 21 21:37:49 2021 +0000 +++ b/tool_data_table_conf.xml.sample Tue Mar 28 18:54:12 2023 +0000 @@ -1,6 +1,6 @@ <tables> - <table name="metaphlan_database" comment_char="#"> - <columns>value, name, dbkey, path</columns> - <file path="tool-data/metaphlan_database.loc" /> + <table name="metaphlan_database_versioned" comment_char="#"> + <columns>value, name, dbkey, path, db_version</columns> + <file path="tool-data/metaphlan_database_versioned.loc"/> </table> </tables>
--- a/tool_data_table_conf.xml.test Wed Apr 21 21:37:49 2021 +0000 +++ b/tool_data_table_conf.xml.test Tue Mar 28 18:54:12 2023 +0000 @@ -1,6 +1,6 @@ <tables> - <table name="metaphlan_database" comment_char="#"> - <columns>value, name, dbkey, path</columns> - <file path="${__HERE__}/test-data/metaphlan_database.loc" /> + <table name="metaphlan_database_versioned" comment_char="#"> + <columns>value, name, dbkey, path, db_version</columns> + <file path="${__HERE__}/test-data/metaphlan_database_versioned.loc"/> </table> -</tables> \ No newline at end of file +</tables>