[2] | 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_test" tool_type="data_source" version="1.0.1"> |
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| 11 | <description>Test 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://test.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 test 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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