details: http://www.bx.psu.edu/hg/galaxy/rev/0cf5c25d1d2b changeset: 2447:0cf5c25d1d2b user: ianschenck@Thugunit.local date: Thu Apr 23 14:42:35 2009 -0400 description: Missed adding chrominfo.py, due to my hardcoded paths in test environ. Should be good now? 2 file(s) affected in this change: lib/galaxy/datatypes/chrominfo.py tools/annotation_profiler/annotation_profiler.xml diffs (29 lines): diff -r 854ec7739cfd -r 0cf5c25d1d2b lib/galaxy/datatypes/chrominfo.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/chrominfo.py Thu Apr 23 14:42:35 2009 -0400 @@ -0,0 +1,14 @@ +import data +from galaxy import util +from galaxy.datatypes.sniff import * +from galaxy.web import url_for +from tabular import Tabular +from galaxy.datatypes import metadata +from galaxy.datatypes.metadata import MetadataElement + + +class ChromInfo( Tabular ): + file_ext = "len" + MetadataElement( name="chrom", default=1, desc="Chrom column", param=metadata.ColumnParameter ) + MetadataElement( name="length", default=2, desc="Length column", param=metadata.ColumnParameter ) + diff -r 854ec7739cfd -r 0cf5c25d1d2b tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml Thu Apr 23 13:46:52 2009 -0400 +++ b/tools/annotation_profiler/annotation_profiler.xml Thu Apr 23 14:42:35 2009 -0400 @@ -1,6 +1,6 @@ <tool id="Annotation_Profiler_0" name="Profile Annotations" Version="1.0.0"> <description>for a set of genomic intervals</description> - <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len -b 3 -t $table_names</command> + <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${chromInfo} -b 3 -t $table_names</command> <inputs> <param format="interval" name="input1" type="data" label="Choose Intervals"> <validator type="dataset_metadata_in_file" filename="annotation_profiler_valid_builds.txt" metadata_name="dbkey" metadata_column="0" message="Profiling is not currently available for this species."/>