changeset 7:b82d4034e0f8 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Tue Feb 11 17:51:48 2014 -0500
@@ -0,0 +1,9 @@
+## What is it?
+Galaxy datatype and display-application definitions for Proteomics data
+
+## Installation
+Install into your local galaxy instance from the main galaxy toolshed at http://toolshed.g2.bx.psu.edu/
+
+To visualize data you will need to install the protviz visualization web application.  This is available at
+[https://bitbucket.org/Andrew_Brock/proteomics-visualise](https://bitbucket.org/Andrew_Brock/proteomics-visualise)
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/display_applications/proteomics/ProtGff.xml	Tue Feb 11 17:51:48 2014 -0500
@@ -0,0 +1,18 @@
+<display id="proteomics_gff" version="1.0.0" name="view gff in">
+        <dynamic_links from_file="tool-data/proteogenomics_display_site.txt" skip_startswith="#" id="0" name="0">
+        <!-- Define parameters by column from file -->
+        <dynamic_param name="site_id" value="0"/>
+        <dynamic_param name="site_url" value="1"/>
+        <!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
+        <url target_frame="galaxy_main">${site_url}/init_local?file=${encoded_filename.qp}&amp;type=protgff</url>
+        <param type="data" name="prot_file" viewable="False" format="protgff"/>
+        <param type="data" dataset="prot_file" name="protgff_file" format="protgff" viewable="False" />
+        <param type="template" name="encoded_filename" strip="True" >
+            #import binascii
+            ${binascii.hexlify( $protgff_file.file_name )}
+        </param>
+        <param type="template" name="galaxy_url" strip="True" >
+                ${BASE_URL.split(":")[1][2:]}
+        </param>
+    </dynamic_links>
+</display>
\ No newline at end of file

--- a/proteomics.py	Fri Feb 07 09:21:34 2014 -0500
+++ b/proteomics.py	Tue Feb 11 17:51:48 2014 -0500
@@ -6,6 +6,7 @@
 import binascii
 
 from galaxy.datatypes.sniff import *
+from galaxy.datatypes import data
 from galaxy.datatypes.data import Text
 from galaxy.datatypes.xml import GenericXml
 from galaxy.datatypes.binary import Binary

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/proteogenomics_display_site.txt.sample	Tue Feb 11 17:51:48 2014 -0500
@@ -0,0 +1,3 @@
+#Proteomic Visualization application should be hosted on the same server as galaxy
+#Entries in this file are of the format "site_id" site_url
+Proteogenomics Browser	http://127.0.0.1:8600