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1 <?xml version="1.0"?>
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2 <!--
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3 If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
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4 the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
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5 initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
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6 -->
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7 <tool name="Germinate 3" id="germinate_importer" tool_type="data_source" version="1.0.0">
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8 <description>import data from a Germinate 3 instance</description>
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9 <!--<command><![CDATA[
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10 cat $output
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11 ]]></command>-->
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12
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13 <command><![CDATA[
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14 java -jar $__tool_directory__/germinate-lib/germinate-galaxy.jar $map $genotypes
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15 ]]>
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16 </command>
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17
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18 <!--<inputs action="http://bioinf.hutton.ac.uk/galaxy/test.html" check_values="false" method="get" target="galaxy_main">-->
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19 <!--<inputs action="http://143.234.98.86:8080/germinate-demo-dev/" check_values="false" method="get" target="galaxy_main">-->
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20 <inputs action="http://bioinf.hutton.ac.uk/galaxy-germinate" check_values="false" method="get">
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21 <display>Download from Germinate</display>
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22 <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
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23 <param name="tool_id" type="hidden" value="germinate_importer" />
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24 <!--<param name="wibble" type="hidden" value="1" />
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25 <param name="wobble" type="hidden" value="2" />
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26 <param name="flump" type="hidden" value="3" />-->
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27 </inputs>
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28 <request_param_translation>
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29 <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
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30 <request_param galaxy_name="URL" remote_name="extraction" missing="" />
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31 <!--<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" >-->
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32 <!--<value_translation>
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33 <value galaxy_value="auto" remote_value="primaryTable" />
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34 <value galaxy_value="auto" remote_value="selectedFields" />
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35 <value galaxy_value="wig" remote_value="wigData" />
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36 <value galaxy_value="interval" remote_value="tab" />
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37 <value galaxy_value="html" remote_value="hyperlinks" />
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38 <value galaxy_value="fasta" remote_value="sequence" />
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39 <value galaxy_value="gtf" remote_value="gff" />
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40 </value_translation>
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41 </request_param>-->
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42 </request_param_translation>
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43 <uihints minwidth="800"/>
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44 <outputs>
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45 <!--<data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/>-->
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46 <data name="map" format="fjmap" label="${tool.name}"/>
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47 <data name="genotypes" format="fjgenotype" label="${tool.name}"/>
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48 </outputs>
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49 <options sanitize="False" refresh="True"/>
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50 <citations>
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51 <citation type="doi">10.1093/database/bar011</citation>
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52 <citation type="doi">10.1101/gr.229102</citation>
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53 </citations>
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54 </tool>
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