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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="PRIDE BioMart" id="pride_biomart" tool_type="data_source" version="0.1.0">
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8 <description>Download proteomic data from the EBI Pride BioMart.</description>
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9 <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
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10 <inputs action="http://www.ebi.ac.uk/pride/biomart/martview" check_values="false" method="get" target="_top">
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11 <display>$GALAXY_URL</display>
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12 <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" />
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13 </inputs>
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14 <request_param_translation>
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15 <request_param galaxy_name="URL" remote_name="URL" missing="">
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16 <append_param separator="&" first_separator="?" join="=">
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17 <value name="_export" missing="1" />
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18 <value name="GALAXY_URL" missing="0" />
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19 </append_param>
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20 </request_param>
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21 <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
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22 <value_translation>
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23 <value galaxy_value="tabular" remote_value="TSV" />
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24 </value_translation>
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25 </request_param>
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26 <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
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27 <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" />
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28 <request_param galaxy_name="organism" remote_name="organism" missing="" />
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29 <request_param galaxy_name="table" remote_name="table" missing="" />
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30 <request_param galaxy_name="description" remote_name="description" missing="" />
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31 <request_param galaxy_name="name" remote_name="name" missing="Rice mart query" />
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32 <request_param galaxy_name="info" remote_name="info" missing="" />
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33 </request_param_translation>
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34 <uihints minwidth="800"/>
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35 <outputs>
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36 <data name="output" format="tabular" />
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37 </outputs>
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38 <options sanitize="False" refresh="True"/>
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39 </tool>
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