12:59 p.m.
details: http://www.bx.psu.edu/hg/galaxy/rev/5c2d30d3fb04
changeset: 2420:5c2d30d3fb04
user: Greg Von Kuster <greg(a)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>