[26.0] Add new datatypes: .taf and .taf.gz

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

@@ -31,6 +31,7 @@
     <datatype extension="anvio_variability" type="galaxy.datatypes.tabular:TSV" display_in_upload="false" subclass="true" />
     <datatype extension="arff" type="galaxy.datatypes.text:Arff" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="paf" auto_compressed_types="gz" type="galaxy.datatypes.text:Paf" mimetype="text/plain" display_in_upload="true"/>
+    <datatype extension="taf" auto_compressed_types="gz" type="galaxy.datatypes.text:Taf" mimetype="text/plain"  display_in_upload="true" description="Transposed Alignment Format. The first line of a .taf file begins with #taf. This word is followed by white-space-separated 'variable:value' pairs. There should be no white space surrounding the ':'." description_url="https://github.com/ComparativeGenomicsToolkit/taffy/blob/main/docs/taf_format.md"/>
     <datatype extension="gfa1" auto_compressed_types="gz" type="galaxy.datatypes.text:Gfa1" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="gfa2" auto_compressed_types="gz" type="galaxy.datatypes.text:Gfa2" mimetype="text/plain" display_in_upload="true">
         <infer_from suffix="gfa" />
@@ -1412,6 +1413,7 @@
     <sniffer type="galaxy.datatypes.tabular:Pileup"/>
     <sniffer type="galaxy.datatypes.tabular:Psl"/>
     <sniffer type="galaxy.datatypes.text:Paf"/>
+    <sniffer type="galaxy.datatypes.text:Taf"/>
     <sniffer type="galaxy.datatypes.interval:Interval"/>
     <sniffer type="galaxy.datatypes.tabular:FourDNPairs"/>
     <sniffer type="galaxy.datatypes.tabular:FourDNPairsam"/>

lib/galaxy/datatypes/test/test.taf

@@ -0,0 +1,119 @@
+#taf version:1 scoring:N/A
+GGGGGGGGG ; i 0 Anc0.Anc0refChr0 0 + 4151 i 1 Anc1.Anc1refChr1 292714 + 296994 i 2 Anc2.Anc2refChr1 5 + 4655 i 3 mr.mrrefChr1 178277 + 182340 i 4 simCow_chr6.simCow.chr6 5045 - 602619 i 5 simDog_chr6.simDog.chr6 589129 + 593897 i 6 simHuman_chr6.simHuman.chr6 597375 + 601863 i 7 simMouse_chr6.simMouse.chr6 630640 + 636262 i 8 simRat_chr6.simRat.chr6 642153 + 647215
+TTTTTTTTT
+CCCCGCCCC
+AAAAAAAAA
+AAAAAAAAA
+GGGGGGGGG
+CCCCCCCCC
+TTTTTTTAT
+CCCCCCCTC
+AAATAAATT
+GGGGGGGGG
+TTTTTTTTT
+AATATTAAA
+GGGCGGGCA
+AAAAAGAAA
+TTTTTTTTT
+AAGAGGAAA
+CCCCCCTCG
+TTTTTTTTT
+GGGAGGGAA
+GGGGGGGGG
+AAAAAAAAA
+TTTTTTTTT
+TTTTTTTTT
+AAAGGAAGG
+GGGGGAGGG
+GGGAGGGAA
+AAACAAACC
+AAAAAAAAA
+TTTTCTTTT
+TTTTTTTTT
+CCCCCCCCC
+AAAAAAAAA
+TTTTTTTTT
+GGGGGGAGG
+AAAGAAAGG
+GGGAGGGAA
+TTTTTTTTT
+TTTGTTTGG
+AAAAAAAAA
+AAAAAGACA
+GGGAGGCAA
+CCCCCCCAC
+TTTTTTTTT
+GGGGGGGGG
+TTTTTCTTT
+AAAGAAAGG
+GGGAAGGAC
+CCTCGTCCC
+CCCTCCCTT
+AAAATAAAA ; g 3 1 g 7 1 g 8 1
+AAAAAAAAA ; g 4 1
+CCCCTCCCC
+AAAAAAAAA
+TTTATTTAA
+CCCACCCAA
+TTTACTGAA
+GGGAGGGAA
+AAAAAAGAA ; g 3 2 g 7 2 g 8 2
+TTTATTTAA
+AAGAGGAAA
+TTTTTTTTT
+AAACAAGCC
+TTTTT-CTT
+TTTTT-TAT
+CCCCC-CCC
+TTTTT-TTC
+CCCTC-ATT
+TTTCT-TCC
+CCACA-CCC
+TTTTT-TTT
+AAAAA-AAA
+AAATA-ATT
+TTTTT-TTT
+AAAAA-AAA
+TTGTG-TTT
+TTTCT-TCC
+TTT-T-T--
+TTT-T-A--
+CCC-C-G--
+TTT-T-T--
+AAA-A-A--
+AAA-A-C--
+TTT-T-T--
+CCC-C-C--
+TTT-T-T--
+TTT-T-T--
+AAAA-A ; d 3 d 6 d 6 g 5 1
+GGGG-G
+TTTT-T
+CCCC-C
+GGGG-G
+AAAA-A
+TTTT-T
+CCCC-G
+TTTT-T
+GGGG-G
+GGGGGG
+GGGGGG
+AAAAAA
+GGG-GAG-- ; i 3 mr.mrrefChr1 178357 + 182340 g 6 6 i 7 simMouse_chr6.simMouse.chr6 630720 + 636262 i 8 simRat_chr6.simRat.chr6 642233 + 647215
+TTT-TTT--
+AAA-AGA--
+CCC-CCA--
+AAAAAAAAA
+GGGGGGGAG
+TTTTTTTTT
+TTTTCTTTT
+TTTTTTTTT
+GGGGGGAGG
+AAAAAAAAA
+TTGTGGTTT
+TTTTTTTT-
+AAAAAAAA-
+TTTTTTTT-
+GGG-GGG--
+TTATAATT-
+CCCCGCCC-

lib/galaxy/datatypes/text.py

@@ -1669,3 +1669,33 @@ def _looks_like_sourmash(self, file_prefix: FilePrefix, load_size: int = 5000) -
         except Exception:
             pass
         return False
+
+
+@build_sniff_from_prefix
+class Taf(Text):
+    """
+    TAF: a Transposed Alignment Format
+
+    https://github.com/ComparativeGenomicsToolkit/taffy/blob/main/docs/taf_format.md
+    """
+
+    file_ext = "taf"
+
+    def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
+        """
+        Determines wether the file is in taf format
+
+        The first line of a .taf file begins with #taf. This word is followed
+        by white-space-separated 'variable:value' pairs. There should be no white
+        space surrounding the ':'.
+
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('test.taf')
+        >>> Taf().sniff(fname)
+        True
+        """
+        try:
+            first_line = next(file_prefix.line_iterator(), "")
+        except Exception:
+            return False
+        return re.search(r"^#taf([ \t]+\S+:\S+)+$", first_line) is not None