From bafb8a9a4d31191a102e5d8c442cbfc82d3ad97e Mon Sep 17 00:00:00 2001
From: Jim Johnson <jj@umn.edu>
Date: Thu, 29 Oct 2015 13:45:40 -0500
Subject: [PATCH 1/3] Add uniprotxml datatype

---
 config/datatypes_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index b7f3b567a86..192c8cf8c8e 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -171,6 +171,7 @@
     <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml" display_in_upload="true" />
     <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true" />
     <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true" />
+    <datatype extension="uniprotxml" type="galaxy.datatypes.proteomics:UniProtXML" mimetype="application/xml" display_in_upload="true" />
     <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp" display_in_upload="true" />
     <datatype extension="splib_noindex" type="galaxy.datatypes.proteomics:SPLibNoIndex" display_in_upload="true" />
     <datatype extension="splib" type="galaxy.datatypes.proteomics:SPLib" display_in_upload="true" />

From 4e6c46fa25cd7f23625d2029b57aad0e67bb732a Mon Sep 17 00:00:00 2001
From: Jim Johnson <jj@umn.edu>
Date: Thu, 29 Oct 2015 13:50:11 -0500
Subject: [PATCH 2/3] Add UniProtXML datatype to proteomics.py

---
 lib/galaxy/datatypes/proteomics.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index ef74b010346..c510e30ae46 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -193,6 +193,12 @@ class TandemXML(ProteomicsXml):
     root = "bioml"
 
 
+class UniProtXML(ProteomicsXml):
+    file_ext = "uniprotxml"
+    blurb = "UniProt Proteome file"
+    root = "uniprot"
+
+
 class Mgf(Text):
     """Mascot Generic Format data"""
     file_ext = "mgf"

From 2a7bba5abaeef0c71c6b86bbbcaf4cdbb0cf7a31 Mon Sep 17 00:00:00 2001
From: Jim Johnson <jj@umn.edu>
Date: Mon, 2 Nov 2015 12:09:18 -0600
Subject: [PATCH 3/3] Add UniProtXML sniffer tag

---
 config/datatypes_conf.xml.sample | 1 +
 1 file changed, 1 insertion(+)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 192c8cf8c8e..00d42d552b9 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -456,6 +456,7 @@
     <sniffer type="galaxy.datatypes.proteomics:TraML"/>
     <sniffer type="galaxy.datatypes.proteomics:MzIdentML"/>
     <sniffer type="galaxy.datatypes.proteomics:MzQuantML"/>
+    <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
     <sniffer type="galaxy.datatypes.proteomics:Msp"/>
     <sniffer type="galaxy.datatypes.proteomics:SPLib"/>
     <sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>