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37 lines
2.0 KiB
XML
37 lines
2.0 KiB
XML
<?xml version="1.0"?>
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<tool name="GenomeSpace Push" id="genomespace_push" tool_type="data_source" force_history_refresh="True" hidden="True" display_interface="False" require_login="True" version="0.0.1">
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<description> - Push data from GenomeSpace to Galaxy</description>
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<environment_variables>
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<environment_variable name="GS_TOKEN">
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#set $token = $__user__.preferences.get( 'genomespace_token', None )
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#assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID or select a valid file via the GenomeSpace browse dialog.' )
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$token
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</environment_variable>
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</environment_variables>
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<command interpreter="python">genomespace_importer.py
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#set $input_file = $URL.split("^")[0] if "^" in $URL else $URL
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#assert $input_file, Exception( 'You must select a valid input file.' )
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--json_parameter_file '${output_file1}'
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--galaxy_root $__root_dir__
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--data_conf $__datatypes_config__
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</command>
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<!-- If using this tool through bioblend, the URL parameter should contain a comma separated list of GenomeSpace URLs -->
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<inputs check_values="False">
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<param name="URL" type="genomespacefile" label="Choose Input File from GenomeSpace" select_type="FILE" />
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</inputs>
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<outputs>
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<data format="auto" name="output_file1" />
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</outputs>
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<help>
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This tool is a variant of the genomespace_importer which behaves like a data_source and allows you to pull data from GenomeSpace.
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The URL parameter must contain a comma separated list of files to pull from GenomeSpace.
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The user must be logged into GenomeSpace through OpenID so that the authentication token can be obtained.
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You can associate your OpenID credentials under the User Preferences panel.
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Click here_ to refresh your GenomeSpace token.
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.. _here: ${static_path}/../user/openid_auth?openid_provider=genomespace&auto_associate=True
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</help>
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<options sanitize="False" refresh="True"/>
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</tool>
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