add unit test to sniffer, minor improvements

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -32,7 +32,7 @@
     <datatype extension="gfa2" auto_compressed_types="gz" type="galaxy.datatypes.text:Gfa2" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format.  Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines.  Blocks are separated from one another by blank lines.  The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
+    <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="A pairwise alignment format." description_url="https://genome.ucsc.edu/goldenPath/help/axt.html"/>
     <datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
     <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
       <converter file="bam_to_bai.xml" target_datatype="bai"/>

lib/galaxy/datatypes/sequence.py

@@ -1205,10 +1205,13 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         >>> fname = get_test_fname( 'alignment.lav' )
         >>> Axt().sniff( fname )
         False
+        >>> fname = get_test_fname( '2.chain' )
+        >>> Axt().sniff( fname )
+        False
         """
         headers = get_headers(file_prefix, None, count=4, comment_designator="#")
         if not (
-            len(headers) == 4
+            len(headers) >= 3
             and len(headers[0]) == 9
             and headers[0][0].isdigit()
             and headers[0][2].isdigit()
@@ -1219,9 +1222,11 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
             and headers[0][8].isdigit()
             and len(headers[1]) == 1
             and len(headers[2]) == 1
-            and headers[3] == []
         ):
             return False
+        # the optional fourth non-comment line has to be empty
+        if len(headers) == 4 and not headers[3] == []:
+            return False
         else:
             return True
 

lib/galaxy/datatypes/test/2.chain

@@ -0,0 +1,10 @@
+##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+##gapPenalties=axtChain O=400 E=30
+chain 67224 chr22 50818468 + 26560645 26561468 chr19 61431566 - 54838449 54839272 1
+823
+
+chain 48985 chr22 50818468 + 26560497 26561116 chr19 61431566 + 29160089 29160708 2
+619
+
+chain 46902 chr22 50818468 + 19792341 19793000 chr19 61431566 + 59180700 59181359 3
+659