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https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Daniel Blankenberg
b2e2b801ea
greater than config.output_size_limit, no data will be retrieved and an error message will be provided to the user. Tools using this script have been updated to provide the max file size on the command line. Resolves ticket #93.
42 lines
2.3 KiB
XML
42 lines
2.3 KiB
XML
<?xml version="1.0"?>
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<!--
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If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
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the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
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initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
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TODO: Hack to get biomart to work - the 'add_to_URL' param can be eliminated when the Biomart team encodes URL prior to sending, meanwhile
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everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
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-->
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<tool name="BioMart" id="biomart" tool_type="data_source" URL_method="get" version="1.0.1">
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<description>Central server</description>
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<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
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<inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
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<display>go to BioMart Central $GALAXY_URL</display>
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<param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
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</inputs>
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<request_param_translation>
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<request_param galaxy_name="URL" remote_name="URL" missing="">
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<add_to_url>
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<param_from_source name="_export" missing="1" />
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<param_from_source name="GALAXY_URL" missing="0" />
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</add_to_url>
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</request_param>
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<request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
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<data_type_translation>
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<format galaxy_format="tabular" remote_format="TSV" />
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</data_type_translation>
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</request_param>
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<request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
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<request_param galaxy_name="organism" remote_name="organism" missing="" />
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<request_param galaxy_name="table" remote_name="table" missing="" />
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<request_param galaxy_name="description" remote_name="description" missing="" />
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<request_param galaxy_name="name" remote_name="name" missing="Biomart query" />
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<request_param galaxy_name="info" remote_name="info" missing="" />
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</request_param_translation>
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<uihints minwidth="800"/>
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<outputs>
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<data name="output" format="tabular" />
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</outputs>
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<options sanitize="False" refresh="True"/>
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</tool>
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