diff ucsc_xenabrowser.xml @ 0:8bb037f88ed2

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsc_xenabrowser.xml	Tue Jan 13 23:37:23 2015 -0500
@@ -0,0 +1,25 @@
+<?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>