Mercurial > repos > iuc > beacon2_import
comparison import.xml @ 0:0a81435a612d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
| author | iuc |
|---|---|
| date | Mon, 22 Jul 2024 12:33:46 +0000 |
| parents | |
| children | e2b10be56bfc |
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| -1:000000000000 | 0:0a81435a612d |
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| 1 <tool id="beacon2_import" name="Beacon2 Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |
| 2 <description>Import JSON formatted datasets to beacon database</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="creators"/> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 ln -s '$input_json_file' ./input.json && | |
| 10 beacon2-import | |
| 11 --input_json_file ./input.json | |
| 12 --db-host $db_host | |
| 13 --db-port $db_port | |
| 14 --database '$database' | |
| 15 --collection '$collection' | |
| 16 --advance-connection | |
| 17 --db-auth-config '$credentials' | |
| 18 $advanced_settings.clearAll | |
| 19 #if $advanced_settings.clearColl: | |
| 20 $advanced_settings.clearColl | |
| 21 --removeCollection $advanced_settings.removeCollection | |
| 22 #end if | |
| 23 > logs.txt | |
| 24 ]]></command> | |
| 25 <expand macro="configfile"/> | |
| 26 <inputs> | |
| 27 <expand macro="Connection_to_MongoDB" /> | |
| 28 <expand macro="Database_Configuration" /> | |
| 29 <param argument="--input_json_file" type="data" format="json" label="INPUT JSON FILE" help="Input the local path to the JSON file or its name on your Galaxy History to import to beacon" /> | |
| 30 <section name="advanced_settings" title="Advanced settings" expanded="false"> | |
| 31 <param argument="--clearAll" type="boolean" checked="false" truevalue="--clearAll" falsevalue="" label="CLEAR ALL COLLECTIONS" help="Delete all data before the new import" /> | |
| 32 <param argument="--clearColl" type="boolean" checked="false" truevalue="--clearColl" falsevalue="" label="CLEAR SPECIFIC COLLECTION" help="Delete specific collection before the new import" /> | |
| 33 <param argument="--removeCollection" optional="true" type="text" label="REMOVED COLLECTION NAME" value="" help="Define the collection name for deletion" /> | |
| 34 </section> | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data name="out_logs" format="txt" label="${tool.name} on ${on_string}: Log file" from_work_dir="logs.txt" /> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 <test expect_num_outputs="1"> | |
| 41 <param name="input_json_file" ftype="json" value="HG00096.json" /> | |
| 42 <param name="db_host" value="20.108.51.167" /> | |
| 43 <param name="database" value="beacon" /> | |
| 44 <param name="collection" value="genomicvarients" /> | |
| 45 <output name="out_logs"> | |
| 46 <assert_contents><has_text_matching expression="inserted"/></assert_contents> | |
| 47 </output> | |
| 48 </test> | |
| 49 </tests> | |
| 50 <help><![CDATA[ | |
| 51 Import JSON formatted datasets to Beacon MongoDB | |
| 52 ]]></help> | |
| 53 <expand macro="citations" /> | |
| 54 </tool> |