From 016a7935a3189e717f58b93bd64aaed8b240795e Mon Sep 17 00:00:00 2001
From: Pierrick Roger <pk.roger@icloud.com>
Date: Mon, 22 Oct 2018 11:07:33 +0200
Subject: [PATCH 1/3] nmrML data type.

---
 config/datatypes_conf.xml.sample   | 1 +
 lib/galaxy/datatypes/proteomics.py | 6 ++++++
 2 files changed, 7 insertions(+)

diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
index 7bbbb1b0a1b..2b1af29a3b9 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -214,6 +214,7 @@
     <datatype extension="tandem" type="galaxy.datatypes.proteomics:TandemXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="thermo.raw" type="galaxy.datatypes.proteomics:ThermoRAW" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="nmrml" type="galaxy.datatypes.proteomics:NmrML" mimetype="application/xml" display_in_upload="true" description="nmrML is an open mark-up language for NMR data." description_url="http://nmrml.org/schema/"/>
     <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf" display_in_upload="true"/>
     <datatype extension="wiff" type="galaxy.datatypes.proteomics:Wiff" display_in_upload="true"/>
     <datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml" display_in_upload="true"/>
diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 4afad30d276..56247371598 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -134,6 +134,12 @@ class MzML(ProteomicsXml):
     blurb = 'mzML Mass Spectrometry data'
     root = "(mzML|indexedmzML)"
 
+class NmrML(ProteomicsXml):
+    """nmrML data"""
+    # No edam format number yet.
+    file_ext = "nmrml"
+    blurb = 'nmrML NMR data'
+    root = "nmrML"
 
 class ProtXML(ProteomicsXml):
     """protXML data"""

From fc6ae3c35eb83fb0e0ca0fd798481b926a1ea2f7 Mon Sep 17 00:00:00 2001
From: David Johnson <djcomlab@gmail.com>
Date: Fri, 26 Oct 2018 11:08:23 +0100
Subject: [PATCH 2/3] Add NmrML to sniffers section

---
 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 2b1af29a3b9..e7555df066c 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -753,6 +753,7 @@
     <sniffer type="galaxy.datatypes.xml:Owl"/>
     <sniffer type="galaxy.datatypes.xml:Sbml"/>
     <sniffer type="galaxy.datatypes.proteomics:MzML"/>
+    <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
     <sniffer type="galaxy.datatypes.proteomics:TandemXML"/>
     <sniffer type="galaxy.datatypes.proteomics:PepXml"/>
     <sniffer type="galaxy.datatypes.proteomics:Mgf"/>

From 7b591bc2098f24d52d2c2cb9d5e32f56cc96afda Mon Sep 17 00:00:00 2001
From: David Johnson <djcomlab@gmail.com>
Date: Fri, 26 Oct 2018 12:25:53 +0100
Subject: [PATCH 3/3] Insert lines to address pep8 problems

---
 lib/galaxy/datatypes/proteomics.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 56247371598..72a0e417f7d 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -134,6 +134,7 @@ class MzML(ProteomicsXml):
     blurb = 'mzML Mass Spectrometry data'
     root = "(mzML|indexedmzML)"
 
+
 class NmrML(ProteomicsXml):
     """nmrML data"""
     # No edam format number yet.
@@ -141,6 +142,7 @@ class NmrML(ProteomicsXml):
     blurb = 'nmrML NMR data'
     root = "nmrML"
 
+
 class ProtXML(ProteomicsXml):
     """protXML data"""
     file_ext = "protxml"