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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 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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8 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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9 -->
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10 <tool name="BioMart" id="biomart" tool_type="data_source" version="1.0.1">
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11 <description>Central server</description>
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12 <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
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13 <inputs action="http://www.biomart.org/biomart/martview" check_values="false" method="get" target="_top">
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14 <display>go to BioMart Central $GALAXY_URL</display>
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15 <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
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16 </inputs>
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17 <request_param_translation>
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18 <request_param galaxy_name="URL" remote_name="URL" missing="">
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19 <append_param separator="&" first_separator="?" join="=">
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20 <value name="_export" missing="1" />
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21 <value name="GALAXY_URL" missing="0" />
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22 </append_param>
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23 </request_param>
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24 <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
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25 <value_translation>
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26 <value galaxy_value="tabular" remote_value="TSV" />
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27 </value_translation>
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28 </request_param>
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29 <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
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30 <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
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31 <request_param galaxy_name="organism" remote_name="organism" missing="" />
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32 <request_param galaxy_name="table" remote_name="table" missing="" />
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33 <request_param galaxy_name="description" remote_name="description" missing="" />
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34 <request_param galaxy_name="name" remote_name="name" missing="Biomart query" />
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35 <request_param galaxy_name="info" remote_name="info" missing="" />
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36 </request_param_translation>
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37 <uihints minwidth="800"/>
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38 <outputs>
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39 <data name="output" format="tabular" />
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40 </outputs>
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41 <options sanitize="False" refresh="True"/>
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42 </tool>
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