details: http://www.bx.psu.edu/hg/galaxy/rev/f802eb92a49a changeset: 1559:f802eb92a49a user: guru date: Fri Oct 17 13:02:26 2008 -0400 description: Added Validator to a bunch of tools..
3 file(s) affected in this change:
tools/extract/liftOver_wrapper.xml tools/extract/phastOdds/phastOdds_tool.xml tools/stats/aggregate_binned_scores_in_intervals.xml
diffs (58 lines):
diff -r f5b051c51295 -r f802eb92a49a tools/extract/liftOver_wrapper.xml --- a/tools/extract/liftOver_wrapper.xml Fri Oct 17 10:46:29 2008 -0400 +++ b/tools/extract/liftOver_wrapper.xml Fri Oct 17 13:02:26 2008 -0400 @@ -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 @@
.. 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.
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diff -r f5b051c51295 -r f802eb92a49a tools/extract/phastOdds/phastOdds_tool.xml --- a/tools/extract/phastOdds/phastOdds_tool.xml Fri Oct 17 10:46:29 2008 -0400 +++ b/tools/extract/phastOdds/phastOdds_tool.xml Fri Oct 17 13:02:26 2008 -0400 @@ -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"> diff -r f5b051c51295 -r f802eb92a49a tools/stats/aggregate_binned_scores_in_intervals.xml --- a/tools/stats/aggregate_binned_scores_in_intervals.xml Fri Oct 17 10:46:29 2008 -0400 +++ b/tools/stats/aggregate_binned_scores_in_intervals.xml Fri Oct 17 13:02:26 2008 -0400 @@ -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">