details: http://www.bx.psu.edu/hg/galaxy/rev/29b6fac01d78 changeset: 3144:29b6fac01d78 user: Greg Von Kuster <greg@bx.psu.edu> date: Thu Dec 03 15:33:15 2009 -0500 description: Add datasource tool configs for modMine and Ratmine. diffstat: tool_conf.xml.main | 2 ++ tool_conf.xml.sample | 6 ++++-- tools/data_source/modmine.xml | 30 ++++++++++++++++++++++++++++++ tools/data_source/ratmine.xml | 29 +++++++++++++++++++++++++++++ 4 files changed, 65 insertions(+), 2 deletions(-) diffs (97 lines): diff -r 7aaa791a6283 -r 29b6fac01d78 tool_conf.xml.main --- a/tool_conf.xml.main Thu Dec 03 14:39:21 2009 -0500 +++ b/tool_conf.xml.main Thu Dec 03 15:33:15 2009 -0500 @@ -8,6 +8,8 @@ <tool file="data_source/biomart.xml" /> <tool file="data_source/gramene_mart.xml" /> <tool file="data_source/flymine.xml" /> + <tool file="data_source/modmine.xml" /> + <tool file="data_source/ratmine.xml" /> <tool file="data_source/eupathdb.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> diff -r 7aaa791a6283 -r 29b6fac01d78 tool_conf.xml.sample --- a/tool_conf.xml.sample Thu Dec 03 14:39:21 2009 -0500 +++ b/tool_conf.xml.sample Thu Dec 03 15:33:15 2009 -0500 @@ -9,10 +9,12 @@ <tool file="data_source/biomart.xml" /> <tool file="data_source/biomart_test.xml" /> <tool file="data_source/gramene_mart.xml" /> + <tool file="data_source/flymine.xml" /> + <tool file="data_source/flymine_test.xml" /> + <tool file="data_source/modmine.xml" /> + <tool file="data_source/ratmine.xml" /> <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/eupathdb.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> diff -r 7aaa791a6283 -r 29b6fac01d78 tools/data_source/modmine.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/modmine.xml Thu Dec 03 15:33:15 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="modMine" id="modmine" tool_type="data_source" URL_method="post"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://intermine.modencode.org/" check_values="false" method="get" target="_top"> + <display>go to modMine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modmine" /> + </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="modMine 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> + diff -r 7aaa791a6283 -r 29b6fac01d78 tools/data_source/ratmine.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/ratmine.xml Thu Dec 03 15:33:15 2009 -0500 @@ -0,0 +1,29 @@ +<?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="Ratmine" id="ratmine" tool_type="data_source" URL_method="post"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get" target="_top"> + <display>go to Ratmine server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" /> + </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="Ratmine 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>