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This commit is contained in:
Daniel Blankenberg
2008-10-17 13:33:46 -04:00
parent 27562d6164 1b6d17978c
commit c0ebad5659
10 changed files with 29 additions and 24 deletions
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datatypes_conf.xml.sample
-1
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@@ -150,7 +150,6 @@
<sniffer order="05" type="galaxy.datatypes.sequence:Maf"/>
<sniffer order="10" type="galaxy.datatypes.sequence:Lav"/>
<sniffer order="15" type="galaxy.datatypes.sequence:Fasta"/>
<sniffer order="20" type="galaxy.datatypes.sequence:Fastq"/>
<sniffer order="25" type="galaxy.datatypes.sequence:FastqSolexa"/>
<sniffer order="30" type="galaxy.datatypes.interval:Wiggle"/>
<sniffer order="35" type="galaxy.datatypes.images:Html"/>
lib/galaxy/tools/__init__.py
+17 -11
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@@ -23,6 +23,7 @@ from galaxy.tools.test import ToolTestBuilder
from galaxy.tools.actions import DefaultToolAction
from galaxy.model import directory_hash_id
from galaxy.util.none_like import NoneDataset
from galaxy.datatypes import sniff
log = logging.getLogger( __name__ )
@@ -1140,22 +1141,21 @@ class Tool:
description = param_dict.get( 'position', '' )
if not description:
description = 'unknown position'
data_type = param_dict.get( 'data_type ')
data_type = param_dict.get( 'data_type' )
items = out_data.items()
for name, data in items:
if organism and table and description:
data.name = '%s on %s: %s (%s)' % ( data.name, organism, table, description )
data.info = info
data.dbkey = dbkey
ext = data_type
try:
ext = data_type_to_ext[ data_type ]
try:
data_type = data_type_to_ext[ data_type ]
except:
pass
if ext not in app.datatypes_registry.datatypes_by_extension:
ext = 'interval'
data = app.datatypes_registry.change_datatype( data, ext )
# store external data source's request parameters temporarily in output file
if data_type not in app.datatypes_registry.datatypes_by_extension:
data_type = 'interval'
data = app.datatypes_registry.change_datatype( data, data_type )
# Store external data source's request parameters temporarily in output file
out = open( data.file_name, 'w' )
for key, value in param_dict.items():
print >> out, '%s\t%s' % ( key, value )
@@ -1168,9 +1168,15 @@ class Tool:
# tag set in the tool config.
if self.tool_type == 'data_source':
name, data = out_data.items()[0]
if data.state == data.states.OK and not data.info:
data.info = data.name
if not isinstance( data.datatype, datatypes.interval.Bed ) and isinstance( data.datatype, datatypes.interval.Interval ):
if data.state == data.states.OK:
data.name = param_dict.get( 'name', data.name )
data.info = param_dict.get( 'info', data.name )
data.dbkey = param_dict.get( 'dbkey', data.dbkey )
data.extension = param_dict.get( 'data_type', data.extension )
if data.extension == 'txt':
data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order )
data = app.datatypes_registry.change_datatype( data, data_type )
elif not isinstance( data.datatype, datatypes.interval.Bed ) and isinstance( data.datatype, datatypes.interval.Interval ):
data.set_meta()
if data.missing_meta():
data = app.datatypes_registry.change_datatype( data, 'tabular' )
lib/galaxy/util/none_like.py
+1 -1
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@@ -23,7 +23,7 @@ class NoneDataset( RecursiveNone ):
if datatypes_registry is None: datatypes_registry = Registry()
self.datatype = datatypes_registry.get_datatype_by_extension( ext )
self._metadata = None
self.metadata = MetadataCollection( self, self.datatype.metadata_spec )
self.metadata = MetadataCollection( self )
def __getattr__( self, name ):
return "None"
def missing_meta( self ):
tools/data_source/flymine.xml
+1 -1
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@@ -14,7 +14,7 @@
<request_param galaxy_name="description" remote_name="description" missing="" />
<request_param galaxy_name="name" remote_name="name" missing="FlyMine query" />
<request_param galaxy_name="info" remote_name="info" missing="" />
<request_param galaxy_name="data_type" remote_name="data_type" missing="interval" />
<request_param galaxy_name="data_type" remote_name="data_type" missing="txt" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
tools/data_source/ucsc_tablebrowser.xml
+1 -1
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@@ -16,7 +16,7 @@
<request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
<request_param galaxy_name="table" remote_name="hgta_track" missing="unknown table" />
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" />
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
tools/data_source/ucsc_tablebrowser_archaea.xml
+1 -1
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@@ -16,7 +16,7 @@
<request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
<request_param galaxy_name="table" remote_name="hgta_track" missing="" />
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" />
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
tools/data_source/ucsc_tablebrowser_test.xml
+1 -1
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@@ -16,7 +16,7 @@
<request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
<request_param galaxy_name="table" remote_name="hgta_track" missing="" />
<request_param galaxy_name="description" remote_name="hgta_regionType" missing="" />
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="interval" />
<request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="bed" />
</request_param_translation>
<uihints minwidth="800"/>
<outputs>
tools/extract/liftOver_wrapper.xml
+4 -7
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@@ -3,7 +3,8 @@
<command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey</command>
<inputs>
<param format="interval" name="input" type="data" label="Convert coordinates of">
<validator type="unspecified_build" />
<validator type="unspecified_build" />
<validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
</param>
<param name="to_dbkey" type="select" label="To">
<options from_file="liftOver.loc">
@@ -11,7 +12,7 @@
<column name="value" index="2"/>
<column name="dbkey" index="0"/>
<filter type="data_meta" ref="input" key="dbkey" column="0" />
</options>
</options>
</param>
</inputs>
<outputs>
@@ -39,11 +40,7 @@ Make sure that the genome build of the input dataset is specified (click the pen
.. class:: warningmark
The **To** list will be empty if we don't carry any liftover mappings corresponding to the genome build of the input dataset.
.. class:: warningmark
This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. If this is not the case, it will return empty output datasets.
This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. If this is not the case with any line of the input dataset, the tool will return empty output datasets.
-----
tools/extract/phastOdds/phastOdds_tool.xml
+1
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@@ -4,6 +4,7 @@
<inputs>
<param format="interval" name="input" type="data" label="Interval file">
<validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg17. Click the pencil icon in your history item to set the genome build."/>
<validator type="dataset_metadata_in_file" filename="phastOdds.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." />
</param>
<param name="score_file" type="select" label="Available datasets">
<options from_file="phastOdds.loc">
tools/stats/aggregate_binned_scores_in_intervals.xml
+2
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@@ -8,6 +8,8 @@
<inputs>
<param format="interval" name="input1" type="data" label="Interval file">
<validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg16, hg17 or hg18. Click the pencil icon in your history item to set the genome build."/>
<validator type="dataset_metadata_in_file" filename="binned_scores.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build." />
</param>
<conditional name="score_source_type">
<param name="score_source" type="select" label="Score Source">