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https://github.com/galaxyproject/galaxy.git
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Wolfgang Maier
bd0f257452
Allows moving all data source tools using the script to profile 20.09. For more recent profiles data_source.py would have to work outside of Galaxy's Python environment.
52 lines
2.9 KiB
XML
52 lines
2.9 KiB
XML
<?xml version="1.0"?>
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<!--
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hacked from biomart.xml - testing hapmap biomart - problem is going to be converting these to lped/pbed
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the data returned will be in all sorts of different shapes - and the sample ids need to be obtained separately
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to create reliable pedigrees. eesh...
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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="HapMapMart" id="hapmapmart" tool_type="data_source" version="0.0.01" profile="20.09">
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<description>HapMap Biomart</description>
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<edam_operations>
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<edam_operation>operation_0224</edam_operation>
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</edam_operations>
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<command><![CDATA[
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python '$__tool_directory__/data_source.py' '$output' $__app__.config.output_size_limit
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]]></command>
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<inputs action="http://hapmap.ncbi.nlm.nih.gov/biomart/martview" check_values="false" method="get" target="_top">
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<display>go to HapMap BioMart $GALAXY_URL</display>
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<param name="GALAXY_URL" type="baseurl" value="/tool_runner/hapmapmart" />
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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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<append_param separator="&" first_separator="?" join="=">
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<value name="_export" missing="1" />
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<value name="GALAXY_URL" missing="0" />
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</append_param>
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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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<value_translation>
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<value galaxy_value="tabular" remote_value="TSV" />
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</value_translation>
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</request_param>
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<request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
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<request_param galaxy_name="dbkey" remote_name="dbkey" missing="hg18" />
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<request_param galaxy_name="organism" remote_name="organism" missing="human" />
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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="HapMap 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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