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1 <?xml version="1.0"?>
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2 <!--
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3 hacked from biomart.xml - testing hapmap biomart - problem is going to be converting these to lped/pbed
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4 the data returned will be in all sorts of different shapes - and the sample ids need to be obtained separately
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5 to create reliable pedigrees. eesh...
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6
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7 If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
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8 the initial response. If value of 'URL_method' is 'post', any additional params coming back in the
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9 initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
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10
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11 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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12 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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13 -->
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14 <tool name="HapMapMart" id="hapmapmart" tool_type="data_source" version="0.0.01">
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15 <description>HapMap Biomart</description>
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16 <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
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17 <inputs action="http://hapmap.ncbi.nlm.nih.gov/biomart/martview" check_values="false" method="get" target="_top">
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18 <display>go to HapMap BioMart $GALAXY_URL</display>
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19 <param name="GALAXY_URL" type="baseurl" value="/tool_runner/hapmapmart" />
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20 </inputs>
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21 <request_param_translation>
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22 <request_param galaxy_name="URL" remote_name="URL" missing="">
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23 <append_param separator="&" first_separator="?" join="=">
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24 <value name="_export" missing="1" />
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25 <value name="GALAXY_URL" missing="0" />
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26 </append_param>
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27 </request_param>
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28 <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
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29 <value_translation>
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30 <value galaxy_value="tabular" remote_value="TSV" />
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31 </value_translation>
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32 </request_param>
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33 <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
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34 <request_param galaxy_name="dbkey" remote_name="dbkey" missing="hg18" />
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35 <request_param galaxy_name="organism" remote_name="organism" missing="human" />
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36 <request_param galaxy_name="table" remote_name="table" missing="" />
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37 <request_param galaxy_name="description" remote_name="description" missing="" />
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38 <request_param galaxy_name="name" remote_name="name" missing="HapMap query" />
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39 <request_param galaxy_name="info" remote_name="info" missing="" />
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40 </request_param_translation>
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41 <uihints minwidth="800"/>
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42 <outputs>
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43 <data name="output" format="tabular" />
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44 </outputs>
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45 <options sanitize="False" refresh="True"/>
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46 </tool>
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