details: http://www.bx.psu.edu/hg/galaxy/rev/511c2b1966dc changeset: 1699:511c2b1966dc user: Greg Von Kuster greg@bx.psu.edu date: Tue Jan 13 10:55:08 2009 -0500 description: Add new tool config for flymine production server.

4 file(s) affected in this change:

tool_conf.xml.main tool_conf.xml.sample tools/data_source/flymine.xml tools/data_source/flymine_test.xml

diffs (68 lines):

diff -r 88fe7fbd28da -r 511c2b1966dc tool_conf.xml.main --- a/tool_conf.xml.main Tue Jan 13 10:34:39 2009 -0500 +++ b/tool_conf.xml.main Tue Jan 13 10:55:08 2009 -0500 @@ -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/flymine.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> </section> diff -r 88fe7fbd28da -r 511c2b1966dc tool_conf.xml.sample --- a/tool_conf.xml.sample Tue Jan 13 10:34:39 2009 -0500 +++ b/tool_conf.xml.sample Tue Jan 13 10:55:08 2009 -0500 @@ -11,6 +11,7 @@ <tool file="data_source/wormbase.xml" /> <tool file="data_source/wormbase_test.xml" /> <tool file="data_source/flymine.xml" /> + <tool file="data_source/flymine_test.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> <tool file="data_source/epigraph_import_test.xml" /> diff -r 88fe7fbd28da -r 511c2b1966dc tools/data_source/flymine.xml --- a/tools/data_source/flymine.xml Tue Jan 13 10:34:39 2009 -0500 +++ b/tools/data_source/flymine.xml Tue Jan 13 10:55:08 2009 -0500 @@ -7,7 +7,7 @@ <tool name="Flymine" id="flymine" tool_type="data_source" URL_method="post"> <description>server</description> <command interpreter="python">data_source.py $output</command> - <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get" target="_top"> + <inputs action="http://www.flymine.org" check_values="false" method="get" target="_top"> <display>go to Flymine server $GALAXY_URL</display> <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> </inputs> diff -r 88fe7fbd28da -r 511c2b1966dc tools/data_source/flymine_test.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/flymine_test.xml Tue Jan 13 10:55:08 2009 -0500 @@ -0,0 +1,30 @@ +<?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. +--> +<tool name="Flymine test" id="flymine_test" tool_type="data_source" URL_method="post"> + <description>server</description> + <command interpreter="python">data_source.py $output</command> + <inputs action="http://preview.flymine.org/preview/begin.do" check_values="false" method="get" target="_top"> + <display>go to Flymine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=flymine" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing="" /> + <request_param galaxy_name="dbkey" remote_name="db" 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="FlyMine query" /> + <request_param galaxy_name="info" remote_name="info" missing="" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> +