removed gbk.gz extension

config/datatypes_conf.xml.sample

@@ -492,9 +492,6 @@
     <datatype extension="genbank.gz" type="galaxy.datatypes.sequence:GenbankGz" display_in_upload="true">
         <converter file="genbankgz_to_genbank.xml" target_datatype="genbank"/>
     </datatype>
-    <datatype extension="gbk.gz" type="galaxy.datatypes.sequence:GbkGz" display_in_upload="true">
-        <converter file="gbkgz_to_genbank.xml" target_datatype="genbank"/>
-    </datatype>
     <datatype extension="hennig86" type="galaxy.datatypes.data:Text" subclass="true"/>
     <datatype extension="ig" type="galaxy.datatypes.data:Text" subclass="true"/>
     <datatype extension="jackknifer" type="galaxy.datatypes.data:Text" subclass="true"/>
@@ -798,7 +795,6 @@
     <sniffer type="galaxy.datatypes.sequence:Axt"/>
     <sniffer type="galaxy.datatypes.sequence:Genbank"/>
     <sniffer type="galaxy.datatypes.sequence:GenbankGz"/>
-    <sniffer type="galaxy.datatypes.sequence:GbkGz"/>
     <sniffer type="galaxy.datatypes.interval:Bed"/>
     <sniffer type="galaxy.datatypes.interval:CustomTrack"/>
     <sniffer type="galaxy.datatypes.interval:Gtf"/>

lib/galaxy/datatypes/converters/gbkgz_to_genbank.xml

@@ -1,11 +0,0 @@
-<tool id="CONVERTER_gbkgz_to_genbank" name="Convert gbk.gz files to genbank" version="1.0.0" hidden="true">
-  <command>gzip -dcf '$input1' > '$output1'</command>
-  <inputs>
-    <param format="gbk.gz" name="input1" type="data" label="Choose Gbk file"/>
-  </inputs>
-  <outputs>
-    <data format="genbank" name="output1"/>
-  </outputs>
-  <help>
-  </help>
-</tool>

lib/galaxy/datatypes/sequence.py

@@ -44,7 +44,6 @@ log = logging.getLogger(__name__)
 SNIFF_COMPRESSED_FASTQS = os.environ.get("GALAXY_ENABLE_BETA_COMPRESSED_FASTQ_SNIFFING", "0") == "1"
 SNIFF_COMPRESSED_FASTAS = os.environ.get("GALAXY_ENABLE_BETA_COMPRESSED_FASTA_SNIFFING", "0") == "1"
 SNIFF_COMPRESSED_GENBANKS = os.environ.get("GALAXY_ENABLE_BETA_COMPRESSED_GENBANK_SNIFFING", "0") == "1"
-SNIFF_COMPRESSED_GBKS = os.environ.get("GALAXY_ENABLE_BETA_COMPRESSED_GBK_SNIFFING", "0") == "1"
 
 
 class SequenceSplitLocations(data.Text):
@@ -1227,22 +1226,6 @@ class GenbankGz(data.Text, CompressedArchive):
         return data.Text.sniff(self, filename)
 
 
-class GbkGz(data.Text, CompressedArchive):
-    """Class representing a generic compressed Genbank sequence"""
-    edam_format = "format_1936"
-    edam_data = "data_0849"
-    file_ext = "gbk.gz"
-    compressed = True
-
-    def sniff(self, filename):
-        """Determines whether the file is in gzip-compressed Genbank format"""
-        if not SNIFF_COMPRESSED_GBKS:
-            return False
-        if not is_gzip(filename):
-            return False
-        return data.Text.sniff(self, filename)
-
-
 class MemePsp(Sequence):
     """Class representing MEME Position Specific Priors"""
     file_ext = "memepsp"