# HG changeset patch
# User melissacline
# Date 1433287002 14400
# Node ID 7c49d9f8687afac4ecce472d3e4dc87d18eb4d57
# Parent  fcef0cd871062e665e2f74692a00f847b25625e5
Deleted selected files, clearing up a merge problem.

diff -r fcef0cd87106 -r 7c49d9f8687a ucsc_xena_datapages.xml
--- a/ucsc_xena_datapages.xml	Tue Jun 02 19:11:39 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<?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="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 $__app__.config.output_size_limit</command>   
-   <inputs action="https://genome-cancer.soe.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_xenadatapages" />
-    </inputs>
-    <request_param_translation>
-        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
-        <request_param galaxy_name="URL" remote_name="URL" missing="" />
-    </request_param_translation>
-    <uihints minwidth="800"/>
-    <outputs>
-        <data name="genomic" format="tabular" label="#echo $URL.rsplit('/',1)[1].rsplit('.',1)[0]+' genomic'" />
-    </outputs>
-    <options sanitize="False" refresh="True"/>
-</tool>
diff -r fcef0cd87106 -r 7c49d9f8687a ucsc_xena_hub.xml
--- a/ucsc_xena_hub.xml	Tue Jun 02 19:11:39 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<?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="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.ucsc.edu/proj/site/hgHeatmap-cavm/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" />
-    </inputs>
-    <request_param_translation>
-        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
-        <request_param galaxy_name="URL" remote_name="URL" missing="" />
-    </request_param_translation>
-    <uihints minwidth="800"/>
-    <outputs>
-        <data name="genomic" format="tabular" label="#echo $URL.rsplit('/',1)[1].rsplit('.',1)[0]+' genomic'" />
-    </outputs>
-    <options sanitize="False" refresh="True"/>
-</tool>
diff -r fcef0cd87106 -r 7c49d9f8687a ucsc_xenabrowser.xml
--- a/ucsc_xenabrowser.xml	Tue Jun 02 19:11:39 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-<?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="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.ucsc.edu/proj/site/hgHeatmap-cavm/" 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" />
-    </inputs>
-    <request_param_translation>
-        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="get" />
-        <request_param galaxy_name="URL" remote_name="URL" missing="" />
-    </request_param_translation>
-    <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 fcef0cd87106 -r 7c49d9f8687a xena.jar
Binary file xena.jar has changed