Mercurial > repos > iuc > beacon2_import
view import.xml @ 1:d2646a23f6b2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
author | iuc |
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date | Mon, 19 Aug 2024 10:50:22 +0000 |
parents | 0f85ad162439 |
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<tool id="beacon2_import" name="Beacon2 Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Import JSON formatted datasets to beacon database</description> <macros> <import>macros.xml</import> </macros> <expand macro="creators"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '$input_json_file' ./input.json && beacon2-import --input_json_file ./input.json --db-host $db_host --db-port $db_port --database '$database' --collection '$collection' --advance-connection --db-auth-config '$credentials' $advanced_settings.clearAll #if $advanced_settings.clearColl: $advanced_settings.clearColl --removeCollection $advanced_settings.removeCollection #end if > logs.txt ]]></command> <expand macro="configfile"/> <inputs> <expand macro="Connection_to_MongoDB" /> <expand macro="Database_Configuration" /> <param argument="--input_json_file" type="data" format="json" label="INPUT JSON FILE" help="Input the local path to the JSON file or its name on your Galaxy History to import to beacon" /> <section name="advanced_settings" title="Advanced settings" expanded="false"> <param argument="--clearAll" type="boolean" checked="false" truevalue="--clearAll" falsevalue="" label="CLEAR ALL COLLECTIONS" help="Delete all data before the new import" /> <param argument="--clearColl" type="boolean" checked="false" truevalue="--clearColl" falsevalue="" label="CLEAR SPECIFIC COLLECTION" help="Delete specific collection before the new import" /> <param argument="--removeCollection" optional="true" type="text" label="REMOVED COLLECTION NAME" value="" help="Define the collection name for deletion" /> </section> </inputs> <outputs> <data name="out_logs" format="txt" label="${tool.name} on ${on_string}: Log file" from_work_dir="logs.txt" /> </outputs> <tests> <test expect_num_outputs="1"> <param name="input_json_file" ftype="json" value="HG00096.json" /> <param name="db_host" value="20.108.51.167" /> <param name="database" value="beacon" /> <param name="collection" value="test" /> <output name="out_logs"> <assert_contents><has_text_matching expression="inserted"/></assert_contents> </output> </test> </tests> <help><![CDATA[ Import JSON formatted datasets to Beacon MongoDB ]]></help> <expand macro="citations" /> </tool>