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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_tax_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18 |
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added:
data_manager/data_manager_sylph_tax_database.xml data_manager_conf.xml test-data/sylph_tax_database.loc.test tool-data/sylph_tax_database.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 7862ca465c6b data_manager/data_manager_sylph_tax_database.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_sylph_tax_database.xml Fri May 23 09:48:43 2025 +0000 |
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| @@ -0,0 +1,60 @@ +<tool id="data_manager_sylph_tax_database" name="Download sylph-tax taxonomy metadata files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="@PROFILE@"> + <description></description> + <macros> + <token name="@TOOL_VERSION@">1.2.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> + <token name="@DB_VERSION@">1</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">sylph-tax</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + +mkdir -p '$out_file.extra_files_path'/sylph_tax_metadata_@TOOL_VERSION@ && +sylph-tax download --download-to '$out_file.extra_files_path'/sylph_tax_metadata_@TOOL_VERSION@ && +cp '$dmjson' '$out_file' + ]]></command> + <configfiles> + <configfile name="dmjson"><![CDATA[ +#from datetime import date + +{ + "data_tables":{ + "sylph_tax_database":[ + { + "value": "sylph_tax_downloaded_#echo date.today().strftime('%d%m%Y')#", + "name": "sylph tax database @TOOL_VERSION@", + "path": "sylph_tax_metadata_@TOOL_VERSION@", + "version": "@DB_VERSION@" + } + ] +} + }]]></configfile> + </configfiles> + <inputs> + <param name="version" type="text" label="Version" value="@TOOL_VERSION@" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" label="${tool.name}"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <output name="out_file"> + <assert_contents> + <has_text text='"sylph_tax_database":'/> + <has_text_matching expression='"value": "sylph_tax_downloaded_[0-9]{8}"'/> + <has_text text='"name": "sylph tax database @TOOL_VERSION@"'/> + <has_text_matching expression='"path": "sylph_tax_metadata_@TOOL_VERSION@"'/> + <has_text text='"version": "@DB_VERSION@"'/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +This tool downloads sylph-tax taxonomy metadata files for pre-built databases. + ]]></help> + <citations> + <citation type="doi">10.1038/s41587-024-02412-y</citation> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 7862ca465c6b data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager_conf.xml Fri May 23 09:48:43 2025 +0000 |
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| @@ -0,0 +1,20 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager/data_manager_sylph_tax_database.xml" id="data_manager_sylph_tax_database"> + <data_table name="sylph_tax_database"> <!-- Defines a Data Table to be modified. --> + <output> <!-- Handle the output of the Data Manager Tool --> + <column name="value"/> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="name"/> <!-- columns that are going to be specified by the Data Manager Tool --> + <column name="path" output_ref="out_file"> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">sylph_tax/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/sylph_tax/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + <column name="version"/> + </output> + </data_table> + </data_manager> +</data_managers> \ No newline at end of file |
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| diff -r 000000000000 -r 7862ca465c6b test-data/sylph_tax_database.loc.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sylph_tax_database.loc.test Fri May 23 09:48:43 2025 +0000 |
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| @@ -0,0 +1,11 @@ +#This is a tab separated file describing the location of StarAMR databases +#used for the StarAMR tool +# +#file has this format (white space characters are TAB characters) +# +#The columns are: +#value name path version +# +#For example +#staramr_downloaded_20241004_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 ResFinder: tag 4.6.0, commit d1e607b, 2024-08-06 - PointFinder: tag 4.1.1, commit 694919f, 2024-08-08 - PlasmidFinder: commit 3e77502, 2024-03-07 (downloaded 20241004) /path/to/data +sylph_tax_downloaded_22052025 sylph tax database 1.2.0 /tmp/tmpebaga2e4/galaxy-dev/tool-data/sylph_tax/sylph_tax_metadata_1.2.0 1 |
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| diff -r 000000000000 -r 7862ca465c6b tool-data/sylph_tax_database.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/sylph_tax_database.loc.sample Fri May 23 09:48:43 2025 +0000 |
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| @@ -0,0 +1,10 @@ +#This is a tab separated file describing the location of StarAMR databases +#used for the StarAMR tool +# +#file has this format (white space characters are TAB characters) +# +#The columns are: +#value name path version +# +#For example +#staramr_downloaded_20241004_resfinder_d1e607b_pointfinder_694919f_plasmidfinder_3e77502 ResFinder: tag 4.6.0, commit d1e607b, 2024-08-06 - PointFinder: tag 4.1.1, commit 694919f, 2024-08-08 - PlasmidFinder: commit 3e77502, 2024-03-07 (downloaded 20241004) /path/to/data \ No newline at end of file |
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| diff -r 000000000000 -r 7862ca465c6b tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri May 23 09:48:43 2025 +0000 |
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| @@ -0,0 +1,6 @@ +<tables> + <table name="sylph_tax_database" comment_char="#"> + <columns>value, name, path, version</columns> + <file path="tool-data/sylph_tax_database.loc"/> + </table> +</tables> \ No newline at end of file |
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| diff -r 000000000000 -r 7862ca465c6b tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri May 23 09:48:43 2025 +0000 |
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| @@ -0,0 +1,6 @@ +<tables> + <table name="sylph_tax_database" comment_char="#"> + <columns>value, name, path, version</columns> + <file path="${__HERE__}/test-data/sylph_tax_database.loc.test"/> + </table> +</tables> \ No newline at end of file |