annotate tools/data_source/hapmapmart.xml @ 1:cdcb0ce84a1b

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<?xml version="1.0"?>
<!--
    hacked from biomart.xml - testing hapmap biomart - problem is going to be converting these to lped/pbed
    the data returned will be in all sorts of different shapes - and the sample ids need to be obtained separately
    to create reliable pedigrees. eesh...

    If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
    the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
    initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.

    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
    everything including and beyond the first '&' is truncated from URL.  They said they'll let us know when this is fixed at their end.
-->
<tool name="HapMapMart" id="hapmapmart" tool_type="data_source" version="0.0.01">
	<description>HapMap Biomart</description>
	<command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
	<inputs action="http://hapmap.ncbi.nlm.nih.gov/biomart/martview" check_values="false" method="get" target="_top">
		<display>go to HapMap BioMart $GALAXY_URL</display>
		<param name="GALAXY_URL" type="baseurl" value="/tool_runner/hapmapmart" />
    </inputs>
    <request_param_translation>
        <request_param galaxy_name="URL" remote_name="URL" missing="">
            <append_param separator="&amp;" first_separator="?" join="=">
                <value name="_export" missing="1" />
                <value name="GALAXY_URL" missing="0" />
            </append_param>
        </request_param>
        <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
            <value_translation>
                <value galaxy_value="tabular" remote_value="TSV" />
            </value_translation>
        </request_param>
        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
        <request_param galaxy_name="dbkey" remote_name="dbkey" missing="hg18" />
        <request_param galaxy_name="organism" remote_name="organism" missing="human" />
        <request_param galaxy_name="table" remote_name="table" missing="" />
        <request_param galaxy_name="description" remote_name="description" missing="" />
        <request_param galaxy_name="name" remote_name="name" missing="HapMap query" />
        <request_param galaxy_name="info" remote_name="info" missing="" />
    </request_param_translation>
	<uihints minwidth="800"/>
	<outputs>
		<data name="output" format="tabular" />
	</outputs>
	<options sanitize="False" refresh="True"/>
</tool>