From 97c16db8245570196b556854570b0c120abcb8b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 2 Aug 2017 21:37:21 +0200
Subject: [PATCH 1/4] Add ImzML composite defintion

---
 lib/galaxy/datatypes/proteomics.py | 38 ++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index de6229b81f9..d0f7192a5ab 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -425,3 +425,41 @@ class XHunterAslFormat(Binary):
 class Sf3(Binary):
     """Class describing a Scaffold SF3 files"""
     file_ext = "sf3"
+
+
+class ImzML(Binary):
+    """
+        Class for imzML files.
+        http://www.imzml.org
+    """
+    file_ext = 'imzml'
+    allow_datatype_change = False
+    composite_type = 'auto_primary_file'
+
+    def __init__(self, **kwd):
+        Binary.__init__(self, **kwd)
+
+        """The metadata"""
+        self.add_composite_file(
+            'imzml',
+            description='The imzML metadata component.',
+            is_binary=False)
+            
+        """The mass spectral data"""
+        self.add_composite_file(
+            'ibd',
+            description='The mass spectral data component.',
+            is_binary=True)
+
+    def generate_primary_file(self, dataset=None):
+        rval = ['<html><head><title>imzML Composite Dataset </title></head><p/>']
+        rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
+        for composite_name, composite_file in self.get_composite_files(dataset=dataset).iteritems():
+            fn = composite_name
+            opt_text = ''
+            if composite_file.get('description'):
+                rval.append('<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % (fn, fn, composite_file.get('description'), opt_text))
+            else:
+                rval.append('<li><a href="%s" type="text/plain">%s</a>%s</li>' % (fn, fn, opt_text))
+        rval.append('</ul></div></html>')
+        return "\n".join(rval)

From e2f69a9c5bc7d11274190e223493d6d12d33afb3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 2 Aug 2017 21:40:39 +0200
Subject: [PATCH 2/4] add imzml to the datatypes conf file

---
 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 056f6a3d383..84c3ec9a89d 100644
--- a/config/datatypes_conf.xml.sample
+++ b/config/datatypes_conf.xml.sample
@@ -240,6 +240,7 @@
     <datatype extension="percout" type="galaxy.datatypes.xml:GenericXml" subclass="true" />
     <datatype extension="hardklor" type="galaxy.datatypes.tabular:Tabular" subclass="true" />
     <datatype extension="kronik" type="galaxy.datatypes.tabular:Tabular" subclass="true" />
+    <datatype extension="imzml" type="galaxy.datatypes.proteomics:ImzML" mimetype="application/xml" display_in_upload="true"/>
     <!-- End Proteomics Datatypes -->
     <datatype extension="netcdf" type="galaxy.datatypes.binary:NetCDF" mimetype="application/octet-stream" display_in_upload="true" description="Format used by netCDF software library for writing and reading chromatography-MS data files." />
     <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/>

From 1d609ca2caa158422adcdee0bbc65e73ce0527d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 2 Aug 2017 21:46:18 +0200
Subject: [PATCH 3/4] add edam format

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

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index d0f7192a5ab..5662cf98ee5 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -432,6 +432,7 @@ class ImzML(Binary):
         Class for imzML files.
         http://www.imzml.org
     """
+    edam_format = "format_3682"
     file_ext = 'imzml'
     allow_datatype_change = False
     composite_type = 'auto_primary_file'

From e768e77392471a60425984ae518fb4f34a0552ee Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Wed, 2 Aug 2017 22:45:40 +0200
Subject: [PATCH 4/4] fix pep8

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

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
index 5662cf98ee5..1d61d1f375a 100644
--- a/lib/galaxy/datatypes/proteomics.py
+++ b/lib/galaxy/datatypes/proteomics.py
@@ -445,7 +445,7 @@ class ImzML(Binary):
             'imzml',
             description='The imzML metadata component.',
             is_binary=False)
-            
+
         """The mass spectral data"""
         self.add_composite_file(
             'ibd',