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71 lines
3.5 KiB
XML
71 lines
3.5 KiB
XML
<tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="1.0">
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<description>a visual SPARQL query builder</description>
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<requirements>
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<container type="docker">askomics/flaskomics-with-dependencies:3.2.1</container>
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</requirements>
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<entry_points>
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<entry_point name="AskOmics instance on $infile.display_name" requires_domain="True">
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<port>5000</port>
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<url>/loginapikey/${__user_name__}</url>
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</entry_point>
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</entry_points>
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<environment_variables>
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<!-- AskOmics user -->
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<environment_variable name="CREATE_USER">true</environment_variable>
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<environment_variable name="USER_FIRST_NAME">${__user_name__}</environment_variable>
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<environment_variable name="USER_LAST_NAME">Galaxy</environment_variable>
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<environment_variable name="USER_USERNAME">${__user_name__}</environment_variable>
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<environment_variable name="USER_EMAIL">${__user_email__}</environment_variable>
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<environment_variable name="USER_APIKEY">${__user_name__}</environment_variable>
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<!-- Galaxy info -->
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<environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
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<environment_variable name="GALAXY_API_KEY" inject="api_key" />
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<!-- AskOmics config -->
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<environment_variable name="DEPMODE">prod</environment_variable>
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<environment_variable name="MAX_CELERY_QUEUE">1</environment_variable>
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<environment_variable name="ASKO_askomics_subtitle">Galaxy</environment_variable>
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<environment_variable name="ASKO_askomics_footer_message">AskOmics Interactive Tool for Galaxy</environment_variable>
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<environment_variable name="ASKO_askomics_data_directory">/tmp/askomics-it</environment_variable>
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<environment_variable name="ASKO_askomics_database_path">/tmp/askomics-it/database.db</environment_variable>
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<environment_variable name="ASKO_triplestore_load_url">http://localhost:5000</environment_variable>
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<!-- Virtuoso config -->
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<environment_variable name="SPARQL_UPDATE">true</environment_variable>
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<!--
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Update the following environment variables according to how much memory you want to allow to virtuoso
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see https://github.com/askomics/flaskomics-docker-compose#configure-virtuoso for help
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-->
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<environment_variable name="VIRT_Parameters_NumberOfBuffers">85000</environment_variable>
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<environment_variable name="VIRT_Parameters_MaxDirtyBuffers">65000</environment_variable>
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</environment_variables>
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<command><![CDATA[
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#import re
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#set link_name = re.sub('[^\w_]', '_', $infile.element_identifier)
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#if $infile.ext == 'tabular':
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#set link_name = $link_name + '.tsv'
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#elif $infile.ext == 'interval':
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#set link_name = $link_name + '.bed'
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#else:
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#set link_name = $link_name + '.' + $infile.ext
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#end if
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mkdir -p /import &&
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ln -s '$infile' '/import/$link_name' &&
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/askomics/start_all.sh
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]]>
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</command>
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<inputs>
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<param name="infile" type="data" optional="true" format="tabular,gff,gff3,interval" label="A dataset to load into AskOmics"/>
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</inputs>
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<outputs>
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<data name="outfile" format="txt" />
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</outputs>
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<tests>
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</tests>
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<help>
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AskOmics is a visual SPARQL query interface supporting both intuitive data integration and
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querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL.
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</help>
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</tool>
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