details: http://www.bx.psu.edu/hg/galaxy/rev/87a9cf297998 changeset: 1668:87a9cf297998 user: Greg Von Kuster greg@bx.psu.edu date: Mon Dec 15 10:37:39 2008 -0500 description: Rename gbrowse_elegans to wormbase_test, add a config for the wormbase production server.

4 file(s) affected in this change:

tool_conf.xml.sample tools/data_source/gbrowse_elegans.xml tools/data_source/wormbase.xml tools/data_source/wormbase_test.xml

diffs (104 lines):

diff -r 3a0b07161c1a -r 87a9cf297998 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Dec 15 09:06:11 2008 -0500 +++ b/tool_conf.xml.sample Mon Dec 15 10:37:39 2008 -0500 @@ -9,7 +9,8 @@ <tool file="data_source/microbial_import.xml" /> <tool file="data_source/biomart.xml" /> <tool file="data_source/biomart_test.xml" /> - <tool file="data_source/gbrowse_elegans.xml" /> + <tool file="data_source/wormbase.xml" /> + <tool file="data_source/wormbase_test.xml" /> <tool file="data_source/flymine.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> diff -r 3a0b07161c1a -r 87a9cf297998 tools/data_source/gbrowse_elegans.xml --- a/tools/data_source/gbrowse_elegans.xml Mon Dec 15 09:06:11 2008 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -<?xml version="1.0"?> -<tool name="C. Elegans" id="gbrowse_elegans" tool_type="data_source" URL_method="get"> - <description>server</description> - <command interpreter="python">data_source.py $output</command> - <inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top"> - <display>go to C. Elegans server $GALAXY_URL</display> - <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=gbrowse_elegans" /> - </inputs> - <request_param_translation> - <request_param galaxy_name="URL" remote_name="URL" missing=""> - <add_to_url> - <param_from_source name="d" missing="" /> - <param_from_source name="dbkey" missing="" /> - <param_from_source name="q" missing="" /> - <param_from_source name="s" missing="" /> - <param_from_source name="t" missing="" /> - </add_to_url> - </request_param> - <request_param galaxy_name="data_type" remote_name="data_type" missing="gff3" /> - </request_param_translation> - <uihints minwidth="800"/> - <outputs> - <data name="output" format="txt" /> - </outputs> - <options sanitize="False" refresh="True"/> -</tool> - diff -r 3a0b07161c1a -r 87a9cf297998 tools/data_source/wormbase.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/wormbase.xml Mon Dec 15 10:37:39 2008 -0500 @@ -0,0 +1,26 @@ +<?xml version="1.0"?> +<tool name="Wormbase" id="wormbase" tool_type="data_source" URL_method="get"> + <description>server</description> + <command interpreter="python">data_source.py $output</command> + <inputs action="http://www.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top"> + <display>go to Wormbase server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <add_to_url> + <param_from_source name="d" missing="" /> + <param_from_source name="dbkey" missing="" /> + <param_from_source name="q" missing="" /> + <param_from_source name="s" missing="" /> + <param_from_source name="t" missing="" /> + </add_to_url> + </request_param> + <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 3a0b07161c1a -r 87a9cf297998 tools/data_source/wormbase_test.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/wormbase_test.xml Mon Dec 15 10:37:39 2008 -0500 @@ -0,0 +1,26 @@ +<?xml version="1.0"?> +<tool name="Wormbase" id="wormbase_test" tool_type="data_source" URL_method="get"> + <description>test server</description> + <command interpreter="python">data_source.py $output</command> + <inputs action="http://dev.wormbase.org/db/seq/gbrowse/c_elegans/" check_values="false" method="get" target="_top"> + <display>go to Wormbase test server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=wormbase_test" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <add_to_url> + <param_from_source name="d" missing="" /> + <param_from_source name="dbkey" missing="" /> + <param_from_source name="q" missing="" /> + <param_from_source name="s" missing="" /> + <param_from_source name="t" missing="" /> + </add_to_url> + </request_param> + <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>