Add wiff.tar extension and sniffer

config/datatypes_conf.xml.sample

@@ -224,6 +224,7 @@
     <datatype extension="brukertdf.tar" type="galaxy.datatypes.binary:TdfTar" display_in_upload="true"/>
     <datatype extension="agilentmasshunter.tar" type="galaxy.datatypes.binary:MassHunterTar" display_in_upload="true"/>
     <datatype extension="watersmasslynxraw.tar" type="galaxy.datatypes.binary:MassLynxTar" display_in_upload="true"/>
+    <datatype extension="wiff.tar" type="galaxy.datatypes.binary:WiffTar" 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"/>
@@ -755,6 +756,7 @@
     <sniffer type="galaxy.datatypes.binary:MassHunterTar"/>
     <sniffer type="galaxy.datatypes.binary:MassLynxTar"/>
     <sniffer type="galaxy.datatypes.binary:YepTar"/>
+    <sniffer type="galaxy.datatypes.binary:WiffTar"/>
     <sniffer type="galaxy.datatypes.binary:Fast5ArchiveGz"/>
     <sniffer type="galaxy.datatypes.binary:Fast5ArchiveBz2"/>
     <sniffer type="galaxy.datatypes.binary:Fast5Archive"/>

lib/galaxy/datatypes/binary.py

@@ -2291,7 +2291,7 @@ class YepTar(BafTar):
 
     def get_signature_file(self):
         return "analysis.yep"
-        
+
     def get_type(self):
         return "Agilent/Bruker YEP directory archive"
 
@@ -2302,7 +2302,7 @@ class TdfTar(BafTar):
 
     def get_signature_file(self):
         return "analysis.tdf"
-        
+
     def get_type(self):
         return "Bruker TDF directory archive"
 
@@ -2313,7 +2313,7 @@ class MassHunterTar(BafTar):
 
     def get_signature_file(self):
         return "msscan.bin"
-        
+
     def get_type(self):
         return "Agilent MassHunter directory archive"
 
@@ -2324,11 +2324,41 @@ class MassLynxTar(BafTar):
 
     def get_signature_file(self):
         return "_func001.dat"
-        
+
     def get_type(self):
         return "Waters MassLynx RAW directory archive"
 
 
+class WiffTar(BafTar):
+    """
+    A tar'd up .wiff/.scan pair containing Sciex WIFF format data
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('some.wiff.tar')
+    >>> WiffTar().sniff(fname)
+    True
+    >>> fname = get_test_fname('brukerbaf.d.tar')
+    >>> WiffTar().sniff(fname)
+    False
+    >>> fname = get_test_fname('test.fast5.tar')
+    >>> WiffTar().sniff(fname)
+    False
+    """
+    file_ext = "wiff.tar"
+
+    def sniff(self, filename):
+        try:
+            if tarfile.is_tarfile(filename):
+                with tarfile.open(filename) as rawtar:
+                    return ".wiff" in [os.path.splitext(os.path.basename(f).lower())[1] for f in rawtar.getnames()]
+            return False
+        except Exception as e:
+            log.warning('%s, sniff Exception: %s', self, e)
+        return False
+
+    def get_type(self):
+        return "Sciex WIFF/SCAN archive"
+
+
 if __name__ == '__main__':
     import doctest
     doctest.testmod(sys.modules[__name__])