details: http://www.bx.psu.edu/hg/galaxy/rev/5bc21675703c changeset: 3238:5bc21675703c user: Greg Von Kuster <greg@bx.psu.edu> date: Thu Jan 14 10:24:37 2010 -0500 description: Add a tool config for the new bx_browser data source tool. diffstat: tool_conf.xml.sample | 1 + tools/data_source/bx_browser.xml | 41 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+), 0 deletions(-) diffs (56 lines): diff -r 201c47c29a6c -r 5bc21675703c tool_conf.xml.sample --- a/tool_conf.xml.sample Thu Jan 14 09:44:58 2010 -0500 +++ b/tool_conf.xml.sample Thu Jan 14 10:24:37 2010 -0500 @@ -5,6 +5,7 @@ <tool file="data_source/ucsc_tablebrowser.xml" /> <tool file="data_source/ucsc_tablebrowser_test.xml" /> <tool file="data_source/ucsc_tablebrowser_archaea.xml" /> + <tool file="data_source/bx_browser.xml" /> <tool file="data_source/microbial_import.xml" /> <tool file="data_source/biomart.xml" /> <tool file="data_source/biomart_test.xml" /> diff -r 201c47c29a6c -r 5bc21675703c tools/data_source/bx_browser.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/bx_browser.xml Thu Jan 14 10:24:37 2010 -0500 @@ -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. +--> +<tool name="BX main" id="bx_browser" tool_type="data_source"> + <description>browser</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://main.genome-browser.bx.psu.edu/" check_values="false" method="get"> + <display>go to BX Browser $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner" /> + <param name="tool_id" type="hidden" value="bx_browser" /> + <param name="sendToGalaxy" type="hidden" value="1" /> + <param name="hgta_compressType" type="hidden" value="none" /> + <param name="hgta_outputType" type="hidden" value="bed" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <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="org" missing="unknown species" /> + <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" /> + <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" /> + <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="tabular" > + <value_translation> + <value galaxy_value="tabular" remote_value="primaryTable" /> + <value galaxy_value="tabular" remote_value="selectedFields" /> + <value galaxy_value="wig" remote_value="wigData" /> + <value galaxy_value="interval" remote_value="tab" /> + <value galaxy_value="html" remote_value="hyperlinks" /> + <value galaxy_value="fasta" remote_value="sequence" /> + </value_translation> + </request_param> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="tabular" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>