<?xml version="1.0"?>
<!--
    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.
-->
<tool name="Germinate 3" id="germinate_importer" tool_type="data_source" version="1.0.0">
    <description>import data from a Germinate 3 instance</description>
	<!--<command><![CDATA[
  cat $output
  ]]></command>-->
  
    <command><![CDATA[
        java -jar $__tool_directory__/germinate-lib/germinate-galaxy.jar $map $genotypes
    ]]>
    </command>
		
    <!--<inputs action="http://bioinf.hutton.ac.uk/galaxy/test.html" check_values="false" method="get" target="galaxy_main">-->
	<!--<inputs action="http://143.234.98.86:8080/germinate-demo-dev/" check_values="false" method="get" target="galaxy_main">-->
	<inputs action="http://bioinf.hutton.ac.uk/galaxy-germinate" check_values="false" method="get">
        <display>Download from Germinate</display>
        <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
        <param name="tool_id" type="hidden" value="germinate_importer" />
        <!--<param name="wibble" type="hidden" value="1" />
        <param name="wobble" type="hidden" value="2" />
        <param name="flump" type="hidden" value="3" />-->
    </inputs>
    <request_param_translation>
        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
        <request_param galaxy_name="URL" remote_name="extraction" missing="" />
        <!--<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" >-->
            <!--<value_translation>
                <value galaxy_value="auto" remote_value="primaryTable" />
                <value galaxy_value="auto" remote_value="selectedFields" />
                <value galaxy_value="wig" remote_value="wigData" />
                <value galaxy_value="interval" remote_value="tab" />
                <value galaxy_value="html" remote_value="hyperlinks" />
                <value galaxy_value="fasta" remote_value="sequence" />
                <value galaxy_value="gtf" remote_value="gff" />
            </value_translation>
        </request_param>-->
    </request_param_translation>
    <uihints minwidth="800"/>
    <outputs>
        <!--<data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/>-->
		<data name="map" format="fjmap" label="${tool.name}"/>
		<data name="genotypes" format="fjgenotype" label="${tool.name}"/>
    </outputs>
    <options sanitize="False" refresh="True"/>
    <citations>
        <citation type="doi">10.1093/database/bar011</citation>
        <citation type="doi">10.1101/gr.229102</citation>
    </citations>
</tool>