/tools/data_source/hapmapmart.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 46 lines · 34 code · 0 blank · 12 comment · 0 complexity · d7ab1df975be1b5a1ba76d2ee9f3f505 MD5 · raw file
- <?xml version="1.0"?>
- <!--
- hacked from biomart.xml - testing hapmap biomart - problem is going to be converting these to lped/pbed
- the data returned will be in all sorts of different shapes - and the sample ids need to be obtained separately
- to create reliable pedigrees. eesh...
- 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.
- 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
- everything including and beyond the first '&' is truncated from URL. They said they'll let us know when this is fixed at their end.
- -->
- <tool name="HapMapMart" id="hapmapmart" tool_type="data_source" version="0.0.01">
- <description>HapMap Biomart</description>
- <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
- <inputs action="http://hapmap.ncbi.nlm.nih.gov/biomart/martview" check_values="false" method="get" target="_top">
- <display>go to HapMap BioMart $GALAXY_URL</display>
- <param name="GALAXY_URL" type="baseurl" value="/tool_runner/hapmapmart" />
- </inputs>
- <request_param_translation>
- <request_param galaxy_name="URL" remote_name="URL" missing="">
- <append_param separator="&" first_separator="?" join="=">
- <value name="_export" missing="1" />
- <value name="GALAXY_URL" missing="0" />
- </append_param>
- </request_param>
- <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" >
- <value_translation>
- <value galaxy_value="tabular" remote_value="TSV" />
- </value_translation>
- </request_param>
- <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
- <request_param galaxy_name="dbkey" remote_name="dbkey" missing="hg18" />
- <request_param galaxy_name="organism" remote_name="organism" missing="human" />
- <request_param galaxy_name="table" remote_name="table" missing="" />
- <request_param galaxy_name="description" remote_name="description" missing="" />
- <request_param galaxy_name="name" remote_name="name" missing="HapMap query" />
- <request_param galaxy_name="info" remote_name="info" missing="" />
- </request_param_translation>
- <uihints minwidth="800"/>
- <outputs>
- <data name="output" format="tabular" />
- </outputs>
- <options sanitize="False" refresh="True"/>
- </tool>