Mercurial > repos > xuebing > sharplabtool
comparison tools/data_source/hapmapmart.xml @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <?xml version="1.0"?> | |
| 2 <!-- | |
| 3 hacked from biomart.xml - testing hapmap biomart - problem is going to be converting these to lped/pbed | |
| 4 the data returned will be in all sorts of different shapes - and the sample ids need to be obtained separately | |
| 5 to create reliable pedigrees. eesh... | |
| 6 | |
| 7 If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in | |
| 8 the initial response. If value of 'URL_method' is 'post', any additional params coming back in the | |
| 9 initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed. | |
| 10 | |
| 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 | |
| 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. | |
| 13 --> | |
| 14 <tool name="HapMapMart" id="hapmapmart" tool_type="data_source" version="0.0.01"> | |
| 15 <description>HapMap Biomart</description> | |
| 16 <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> | |
| 17 <inputs action="http://hapmap.ncbi.nlm.nih.gov/biomart/martview" check_values="false" method="get" target="_top"> | |
| 18 <display>go to HapMap BioMart $GALAXY_URL</display> | |
| 19 <param name="GALAXY_URL" type="baseurl" value="/tool_runner/hapmapmart" /> | |
| 20 </inputs> | |
| 21 <request_param_translation> | |
| 22 <request_param galaxy_name="URL" remote_name="URL" missing=""> | |
| 23 <append_param separator="&" first_separator="?" join="="> | |
| 24 <value name="_export" missing="1" /> | |
| 25 <value name="GALAXY_URL" missing="0" /> | |
| 26 </append_param> | |
| 27 </request_param> | |
| 28 <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular" > | |
| 29 <value_translation> | |
| 30 <value galaxy_value="tabular" remote_value="TSV" /> | |
| 31 </value_translation> | |
| 32 </request_param> | |
| 33 <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" /> | |
| 34 <request_param galaxy_name="dbkey" remote_name="dbkey" missing="hg18" /> | |
| 35 <request_param galaxy_name="organism" remote_name="organism" missing="human" /> | |
| 36 <request_param galaxy_name="table" remote_name="table" missing="" /> | |
| 37 <request_param galaxy_name="description" remote_name="description" missing="" /> | |
| 38 <request_param galaxy_name="name" remote_name="name" missing="HapMap query" /> | |
| 39 <request_param galaxy_name="info" remote_name="info" missing="" /> | |
| 40 </request_param_translation> | |
| 41 <uihints minwidth="800"/> | |
| 42 <outputs> | |
| 43 <data name="output" format="tabular" /> | |
| 44 </outputs> | |
| 45 <options sanitize="False" refresh="True"/> | |
| 46 </tool> |