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60 lines
2.3 KiB
XML
60 lines
2.3 KiB
XML
<tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="0.1">
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<description>a visual SPARQL query builder</description>
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<requirements>
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<container type="docker">quay.io/askomics/askomics-ie:17.12_g19.09</container>
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</requirements>
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<entry_points>
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<entry_point name="AskOmics instance on $infile.display_name" requires_domain="True">
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<port>6543</port>
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<url>/login_api_gie?key=abcd</url>
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</entry_point>
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</entry_points>
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<environment_variables>
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<environment_variable name="GALAXY_URL">${__app__.config.galaxy_infrastructure_url}</environment_variable> <!-- FIXME: Warning: The use of __app__ is deprecated and will break backward compatibility in the near future -->
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<environment_variable name="API_KEY" strip="True">
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#if $__user__:
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#for $api_key in $__user__.api_keys:
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${api_key.key}
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#break
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#end for
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#end if
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</environment_variable>
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</environment_variables>
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<command><![CDATA[
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#import re
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## ToDo: the key could be generated randomly
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export ASKO_load_url='http://localhost:6543' &&
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export ASKOMICS_API_KEY='abcd' &&
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export ASKO_files_dir='/tmp/askomics-ie' &&
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export VIRT_Parameters_NumberOfBuffers='10000' &&
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export VIRT_Parameters_MaxDirtyBuffers='6000' &&
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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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bash /start.sh
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]]>
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</command>
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<inputs>
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<param name="infile" type="data" format="tabular,gff,gff3,bed,interval" label="A datasets with genomic coordinates"/>
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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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