# HG changeset patch
# User melissacline
# Date 1433282155 25200
# Node ID 154a9b440b63172cd1a1de74d5063b539b72c00f
# Parent  6785e729c7ad275edf9f55f1d0dd907ad2a950ea# Parent  c298bb05640e7e7f6e74104d5a3fcdc5555707b7
Updated the xena jar to version 14, updated the URL of the Xena pages

diff -r c298bb05640e -r 154a9b440b63 ucsc_xena_datapages.xml
--- a/ucsc_xena_datapages.xml	Thu Apr 23 08:45:54 2015 -0700
+++ b/ucsc_xena_datapages.xml	Tue Jun 02 14:55:55 2015 -0700
@@ -4,13 +4,13 @@
     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="Explore Data in Xena" id="ucsc_xena_datapages" tool_type="data_source">
+<tool name="Explore Data in Xena" id="ucsc_xenadatapages" tool_type="data_source">
     <description>Browse the UCSC Xena Data Pages.</description>
-    <command interpreter="python">ucsc_xena_download.py $genomic $clinical $__app__.config.output_size_limit</command>   
-    <inputs action="https://genome-cancer.soe.ucsc.edu/proj/site/xena/datapages/" check_values="false" method="get">
-        <display>go to UCSC Xena Data $GALAXY_URL</display>
+    <command interpreter="python">ucsc_xena_download.py $genomic $__app__.config.output_size_limit</command>   
+    <inputs action="https://genome-cancer.ucsc.edu/proj/site/xena/datapages/" check_values="false" method="get">
+        <display>Explore the data in Xena $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
-        <param name="tool_id" type="hidden" value="ucsc_xena_datapages" />
+        <param name="tool_id" type="hidden" value="ucsc_xenadatapages" />
     </inputs>
     <request_param_translation>
         <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
@@ -19,7 +19,6 @@
     <uihints minwidth="800"/>
     <outputs>
         <data name="genomic" format="tabular" label="#echo $URL.rsplit('/',1)[1].rsplit('.',1)[0]+' genomic'" />
-        <data name="clinical" format="tabular" label="#echo $URL.rsplit('/',1)[1].rsplit('.',1)[0]+' clinical'"/>
     </outputs>
     <options sanitize="False" refresh="True"/>
 </tool>
diff -r c298bb05640e -r 154a9b440b63 ucsc_xena_hub.xml
--- a/ucsc_xena_hub.xml	Thu Apr 23 08:45:54 2015 -0700
+++ b/ucsc_xena_hub.xml	Tue Jun 02 14:55:55 2015 -0700
@@ -7,7 +7,7 @@
 <tool name="Xena Data Hub" id="ucsc_xenadatahub" tool_type="data_source">
     <description>Select your Xena Data Hub</description>
     <command interpreter="python">ucsc_xena_download.py $genomic $__app__.config.output_size_limit</command>   
-    <inputs action="https://genome-cancer.soe.ucsc.edu/proj/site/xena/hub/" check_values="false" method="get">
+    <inputs action="https://genome-cancer.ucsc.edu/proj/site/xena/hub/" check_values="false" method="get">
         <display>Select your Xena Data Hub $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
         <param name="tool_id" type="hidden" value="ucsc_xenadatapages" />
diff -r c298bb05640e -r 154a9b440b63 ucsc_xenabrowser.xml
--- a/ucsc_xenabrowser.xml	Thu Apr 23 08:45:54 2015 -0700
+++ b/ucsc_xenabrowser.xml	Tue Jun 02 14:55:55 2015 -0700
@@ -7,7 +7,7 @@
 <tool name="UCSC Xena Browser" id="ucsc_xenabrowser" tool_type="data_source">
     <description>Run the UCSC Xena Browser as a Galaxy tool.</description>
     <command interpreter="python">ucsc_xena_download.py $genomic $clinical $__app__.config.output_size_limit</command>   
-    <inputs action="https://genome-cancer.soe.ucsc.edu/proj/site/xena/heatmap" check_values="false" method="get">
+    <inputs action="https://genome-cancer.ucsc.edu/proj/site/xena/heatmap/" check_values="false" method="get">
         <display>go to UCSC Xena Browser $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
         <param name="tool_id" type="hidden" value="ucsc_xenabrowser" />
diff -r c298bb05640e -r 154a9b440b63 xena.jar
Binary file xena.jar has changed
diff -r c298bb05640e -r 154a9b440b63 xena_utils.pyc
Binary file xena_utils.pyc has changed