add Analyze75 datatype

galaxyproject · Oct 21, 2017 · 72dd4a3 · 72dd4a3
1 parent faa50a2
commit 72dd4a3
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diff --git a/config/datatypes_conf.xml.sample b/config/datatypes_conf.xml.sample
@@ -245,6 +245,7 @@
     <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"/>
+    <datatype extension="analyze75" type="galaxy.datatypes.proteomics:Analyze75" mimetype="application/xml" display_in_upload="true"/>
     <!-- End Proteomics Datatypes -->
     <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>

diff --git a/lib/galaxy/datatypes/proteomics.py b/lib/galaxy/datatypes/proteomics.py
@@ -464,3 +464,50 @@ def generate_primary_file(self, dataset=None):
                 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)
+
+
+class Analyze75(Binary):
+    """
+        Mayo Analyze 7.5 files
+        http://www.imzml.org
+    """
+    file_ext = 'analyze75'
+    allow_datatype_change = False
+    composite_type = 'auto_primary_file'
+
+    def __init__(self, **kwd):
+        Binary.__init__(self, **kwd)
+
+        """The header file. Provides information about dimensions, identification, and processing history."""
+        self.add_composite_file(
+            'hdr',
+            description='The Analyze75 header file.',
+            is_binary=False)
+
+        """The image file.  Image data, whose data type and ordering are described by the header file."""
+        self.add_composite_file(
+            'img',
+            description='The Analyze75 image file.',
+            is_binary=True)
+
+        """The optional t2m file."""
+        self.add_composite_file(
+            't2m',
+            description='The Analyze75 t2m file.',
+            optional='True', is_binary=True)
+
+    def generate_primary_file(self, dataset=None):
+        rval = ['<html><head><title>Analyze75 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.optional:
+                opt_text = ' (optional)'
+            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)
+