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Add the ability to define datatypes in the configuration file.

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Datatypes are defined like:
[galaxy:datatypes]
bed = galaxy.datatypes.interval:Bed
png = galaxy.datatypes.images:Image,image/png

where the mime-type (default of text/plain) can be declared after the class name, as is seen with png.
This commit is contained in:
Daniel Blankenberg
2007-06-01 19:25:19 +00:00
parent 437399fc66
commit 4cbfce361b
17 changed files with 204 additions and 108 deletions
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tools/data_source/ucsc_tablebrowser_code.py
+3 -4
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@@ -21,9 +21,8 @@ def exec_before_job( app, inp_data, out_data, param_dict, tool=None):
ext = outputType
try: ext = outputType_to_ext[outputType]
except: pass
if ext not in datatypes.datatypes_by_extension: ext = 'interval'
data = datatypes.change_datatype(data, ext)
if ext not in app.datatypes_registry.datatypes_by_extension: ext = 'interval'
data = app.datatypes_registry.change_datatype(data, ext)
#store ucsc parameters temporarily in output file
out = open(data.file_name,'w')
@@ -40,6 +39,6 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
if not isinstance(data.datatype, datatypes.interval.Bed) and isinstance(data.datatype, datatypes.interval.Interval):
data.set_meta()
if data.missing_meta(): data = datatypes.change_datatype(data, 'tabular')
if data.missing_meta(): data = app.datatypes_registry.change_datatype(data, 'tabular')
data.set_peek()
data.flush()