# HG changeset patch
# User earlhaminst
# Date 1741649237 0
# Node ID c22276db40255d6deae8a5128ea3a8700787242a
# Parent  ab5611663f32f389f0d35e5c48d6c0621b184ccc
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/main/tools/GAFA/ commit a0d7ab86b86bb764e457767bf8e8bc29868d0cbb

diff -r ab5611663f32 -r c22276db4025 GAFA.xml
--- a/GAFA.xml	Mon Mar 03 17:47:53 2025 +0000
+++ b/GAFA.xml	Mon Mar 10 23:27:17 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="gafa" name="Gene Align and Family Aggregator" version="0.4.0">
+<tool id="gafa" name="Gene Align and Family Aggregator" version="0.4.1" profile="18.09">
     <description>generates an SQLite database that can be visualised with Aequatus</description>
     <requirements>
         <requirement type="package" version="3.13">python</requirement>
diff -r ab5611663f32 -r c22276db4025 datatypes_conf.xml
--- a/datatypes_conf.xml	Mon Mar 03 17:47:53 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-    <datatype_files>
-        <datatype_file name="gafa_datatypes.py"/>
-    </datatype_files>
-    <registration>
-        <datatype extension="gafa.sqlite" type="galaxy.datatypes.gafa_datatypes:GAFASQLite" mimetype="application/octet-stream" display_in_upload="True" />
-    </registration>
-    <sniffers>
-        <sniffer type="galaxy.datatypes.gafa_datatypes:GAFASQLite"/>
-    </sniffers>
-</datatypes>
diff -r ab5611663f32 -r c22276db4025 gafa_datatypes.py
--- a/gafa_datatypes.py	Mon Mar 03 17:47:53 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-import logging
-
-from galaxy.datatypes.binary import Binary, SQlite
-from galaxy.datatypes.metadata import MetadataElement, MetadataParameter
-from galaxy.util import sqlite
-
-log = logging.getLogger(__name__)
-
-
-class GAFASQLite(SQlite):
-    """Class describing a GAFA SQLite database"""
-    MetadataElement(name='gafa_schema_version', default='0.1.0', param=MetadataParameter, desc='GAFA schema version',
-                    readonly=True, visible=True, no_value='0.1.0')
-    file_ext = 'gafa.sqlite'
-
-    def set_meta(self, dataset, overwrite=True, **kwd):
-        super(GAFASQLite, self).set_meta(dataset, overwrite=overwrite, **kwd)
-        try:
-            conn = sqlite.connect(dataset.file_name)
-            c = conn.cursor()
-            version_query = 'SELECT version FROM meta'
-            results = c.execute(version_query).fetchall()
-            if len(results) == 0:
-                raise Exception('version not found in meta table')
-            elif len(results) > 1:
-                raise Exception('Multiple versions found in meta table')
-            dataset.metadata.gafa_schema_version = results[0][0]
-        except Exception as e:
-            log.warn("%s, set_meta Exception: %s", self, e)
-
-    def sniff(self, filename):
-        if super(GAFASQLite, self).sniff(filename):
-            gafa_table_names = frozenset(['gene', 'gene_family', 'gene_family_member', 'meta', 'transcript'])
-            conn = sqlite.connect(filename)
-            c = conn.cursor()
-            tables_query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
-            results = c.execute(tables_query).fetchall()
-            found_table_names = frozenset(_[0] for _ in results)
-            return gafa_table_names <= found_table_names
-        return False
-
-
-# Since in Galaxy < 18.01 Binary.register_sniffable_binary_format() ignores the
-# sniff order declared in datatypes_conf.xml and put TS datatypes at the end,
-# instead of simply doing:
-# Binary.register_sniffable_binary_format("sqlite", "sqlite", SQlite)
-# we need to register specialized SQLite datatypes before SQlite
-try:
-    for i, format_dict in enumerate(Binary.sniffable_binary_formats):
-        if format_dict['class'] == SQlite:
-            break
-    else:
-        i += 1
-    Binary.sniffable_binary_formats.insert(i, {'type': 'gafa.sqlite', 'ext': 'gafa.sqlite', 'class': GAFASQLite})
-except AttributeError:
-    pass