Merge pull request #4370 from bgruening/mzml

Add imzML datatype

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"/>

lib/galaxy/datatypes/proteomics.py

@@ -425,3 +425,42 @@ 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
+    """
+    edam_format = "format_3682"
+    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)