mirror of
https://github.com/galaxyproject/galaxy.git
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Enis Afgan
85 lines
2.8 KiB
XML
85 lines
2.8 KiB
XML
<tool id="interactive_tool_openrefine" tool_type="interactive" name="OpenRefine" version="0.2">
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<icon src="openrefine.png" />
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<description>Working with messy data</description>
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<requirements>
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<container type="docker">ylebras/openrefine-docker</container>
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</requirements>
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<entry_points>
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<entry_point name="Openrefine visualisation" requires_domain="False" requires_path_in_url="False">
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<port>3333</port>
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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="HISTORY_ID">$__history_id__</environment_variable>
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<environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
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<environment_variable name="GALAXY_WEB_PORT">8080</environment_variable>
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<environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
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<environment_variable name="API_KEY" inject="api_key" />
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</environment_variables>
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<configfiles>
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<configfile name="start_openrefine"><![CDATA[
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exec /OpenRefine/refine -i 0.0.0.0 -m \$GALAXY_MEMORY_MB &
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##Check if openrefine is up to work
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STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>&1)
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while [[ \${STATUS} =~ "refused" ]]
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do
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echo "Waiting for openrefine: \$STATUS \n"
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STATUS=\$(curl --include 'http://127.0.0.1:3333' 2>&1)
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sleep 4
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done
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]]>
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</configfile>
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</configfiles>
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<command detect_errors="aggressive"><![CDATA[
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#if $infile:
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cp '$infile' /import/input.tabular &&
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#end if
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cat '$start_openrefine' &&
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bash '$start_openrefine' &&
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## Createnew project with the dataset
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cd /refine-python &&
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#if $infile:
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python openrefine_create_project_API.py '/import/input.tabular' &&
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#end if
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tail -f /dev/null
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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,tsv" optional="true" label="Input file in tabular format"/>
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</inputs>
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<outputs>
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<data name="outfile" format="tabular" />
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</outputs>
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<tests>
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<test expect_num_outputs="1">
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</test>
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</tests>
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<help><![CDATA[
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`Openrefine <https://openrefine.org/>`_ (previously Google Refine) is a powerful tool for working with messy data:
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cleaning it; transforming it from one format into another; and extending it with web services and external data.
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.. class:: infomark
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Example input file (TAB separated)::
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"name" "longitude" "latitude" "countryCode"
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Accipiter striatus Vieillot, 1808 -60.291838 46.328137 CA
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Accipiter striatus Vieillot, 1808 -114.58927 35.022485 US
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Accipiter striatus Vieillot, 1808 -93.37406 30.00586 US
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Accipiter striatus Vieillot, 1808 -79.336288 43.682218 CA
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Accipiter striatus Vieillot, 1808 -109.156024 31.904185 US
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Accipiter striatus Vieillot, 1808 -71.098031 42.297408 US
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Accipiter striatus Vieillot, 1808 -110.927215 32.18203 US
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]]>
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</help>
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</tool>
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