details: http://www.bx.psu.edu/hg/galaxy/rev/5c2d30d3fb04 changeset: 2420:5c2d30d3fb04 user: Greg Von Kuster <greg@bx.psu.edu> date: Wed May 27 14:19:59 2009 -0400 description: Add tool config for GrameneMart data source. 3 file(s) affected in this change: tool_conf.xml.main tool_conf.xml.sample tools/data_source/gramene_mart.xml diffs (67 lines): diff -r 1acbcbcebeb3 -r 5c2d30d3fb04 tool_conf.xml.main --- a/tool_conf.xml.main Wed May 27 11:15:35 2009 -0400 +++ b/tool_conf.xml.main Wed May 27 14:19:59 2009 -0400 @@ -6,6 +6,7 @@ <tool file="data_source/ucsc_tablebrowser_archaea.xml" /> <tool file="data_source/microbial_import.xml" /> <tool file="data_source/biomart.xml" /> + <tool file="data_source/gramene_mart.xml" /> <tool file="data_source/flymine.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> diff -r 1acbcbcebeb3 -r 5c2d30d3fb04 tool_conf.xml.sample --- a/tool_conf.xml.sample Wed May 27 11:15:35 2009 -0400 +++ b/tool_conf.xml.sample Wed May 27 14:19:59 2009 -0400 @@ -8,6 +8,7 @@ <tool file="data_source/microbial_import.xml" /> <tool file="data_source/biomart.xml" /> <tool file="data_source/biomart_test.xml" /> + <tool file="data_source/gramene_mart.xml" /> <tool file="data_source/wormbase.xml" /> <tool file="data_source/wormbase_test.xml" /> <tool file="data_source/flymine.xml" /> diff -r 1acbcbcebeb3 -r 5c2d30d3fb04 tools/data_source/gramene_mart.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/gramene_mart.xml Wed May 27 14:19:59 2009 -0400 @@ -0,0 +1,41 @@ +<?xml version="1.0"?> +<!-- + 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="GrameneMart" id="gramenemart" tool_type="data_source" URL_method="get" version="1.0.1"> + <description> Central server</description> + <command interpreter="python">data_source.py $output</command> + <inputs action="http://www.gramene.org/biomart/martview" check_values="false" method="get" target="_top"> + <display>go to GrameneMart Central $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner/biomart" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <add_to_url> + <param_from_source name="_export" missing="1" /> + <param_from_source name="GALAXY_URL" missing="0" /> + </add_to_url> + </request_param> + <request_param galaxy_name="data_type" remote_name="exportView_outputformat" missing="tabular"> + <data_type_translation> + <format galaxy_format="tabular" remote_format="TSV" /> + </data_type_translation> + </request_param> + <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" /> + <request_param galaxy_name="organism" remote_name="organism" missing="" /> + <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="Biomart 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>