# HG changeset patch
# User jorrit
# Date 1361315772 18000
# Node ID 9d9a06b511ff8315054ef418983d550bd9f291ba
# Parent  ebf2b433a23938142cbe4017ef082d26a3d89407
Uploaded

diff -r ebf2b433a239 -r 9d9a06b511ff README
--- a/README	Tue Feb 12 15:25:32 2013 -0500
+++ b/README	Tue Feb 19 18:16:12 2013 -0500
@@ -9,3 +9,35 @@
 # GO:TermFinder needs dependencies GraphViz and GD graphics libraries 
 sudo apt-get $APT_OPTS install libgraphviz-perl
 sudo apt-get $APT_OPTS install libgd-gd2-perl
+
+
+--- Term Enrichment related ---
+(currently used - heavily tied to mysql / old data model)
+http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/amigo/amigo/cgi-bin/term_enrichment?view=log
+
+(command line version - file based)
+http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/
+
+http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-dev/trunk/go-db-perl/scripts/go-find-enriched-terms.pl?view=log
+
+--- AmiGO related ---
+
+for AmiGO Manual 
+http://wiki.geneontology.org/index.php/AmiGO_Manual:_Visualize
+
+online tool to play around (current version, has R Wrapper ramigo)
+http://amigo.geneontology.org/cgi-bin/amigo/visualize?mode=client
+
+online tool Amigo2
+http://amigo2.berkeleybop.org/cgi-bin/amigo2/amigo?mode=visualize
+
+entry point Amigo2
+https://github.com/kltm/amigo/blob/master/perl/bin/visualize
+
+--- workflows ---
+
+gene set + ontology + gene associations =
+
+gene products + background set = (good) + (ambiguous) + (no match, missing)
+
+
diff -r ebf2b433a239 -r 9d9a06b511ff go_goose.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/go_goose.xml	Tue Feb 19 18:16:12 2013 -0500
@@ -0,0 +1,18 @@
+<?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="GOOSE test" id="goose" tool_type="data_source" version="0.0.1">
+    <description>server</description>
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="http://amigo2.berkeleybop.org/cgi-bin/amigo2/goose" check_values="false" method="get" target="_top"> 
+        <display>Go to the GOOSE test server at $GALAXY_URL</display>
+    </inputs>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>