diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py index ec4c443c65a..5f367f86102 100644 --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -66,7 +66,7 @@ class Interval(Tabular): MetadataElement(name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter) MetadataElement(name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter) MetadataElement(name="endCol", default=3, desc="End column", param=metadata.ColumnParameter) - MetadataElement(name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0) + MetadataElement(name="strandCol", default=0, desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0) MetadataElement(name="nameCol", desc="Name/Identifier column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0) MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False) @@ -386,7 +386,7 @@ class Bed(Interval): MetadataElement(name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter) MetadataElement(name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter) MetadataElement(name="endCol", default=3, desc="End column", param=metadata.ColumnParameter) - MetadataElement(name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0) + MetadataElement(name="strandCol", default=0, desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0) MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False) MetadataElement(name="viz_filter_cols", desc="Score column for visualization", default=[4], param=metadata.ColumnParameter, optional=True, multiple=True) # do we need to repeat these? they are the same as should be inherited from interval type @@ -567,7 +567,7 @@ class BedStrict(Bed): MetadataElement(name="chromCol", default=1, desc="Chrom column", readonly=True, param=metadata.MetadataParameter) MetadataElement(name="startCol", default=2, desc="Start column", readonly=True, param=metadata.MetadataParameter) # TODO: start and end should be able to be set to these or the proper thick[start/end]? MetadataElement(name="endCol", default=3, desc="End column", readonly=True, param=metadata.MetadataParameter) - MetadataElement(name="strandCol", desc="Strand column (click box & select)", readonly=True, param=metadata.MetadataParameter, no_value=0, optional=True) + MetadataElement(name="strandCol", default=0, desc="Strand column (click box & select)", readonly=True, param=metadata.MetadataParameter, no_value=0, optional=True) MetadataElement(name="nameCol", desc="Name/Identifier column (click box & select)", readonly=True, param=metadata.MetadataParameter, no_value=0, optional=True) MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False) @@ -1423,7 +1423,7 @@ class ENCODEPeak(Interval): MetadataElement(name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter) MetadataElement(name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter) MetadataElement(name="endCol", default=3, desc="End column", param=metadata.ColumnParameter) - MetadataElement(name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0) + MetadataElement(name="strandCol", default=0, desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0) MetadataElement(name="columns", default=3, desc="Number of columns", readonly=True, visible=False) def sniff(self, filename): diff --git a/test/functional/tools/metadata_bed.xml b/test/functional/tools/metadata_bed.xml new file mode 100644 index 00000000000..e8b354fc2be --- /dev/null +++ b/test/functional/tools/metadata_bed.xml @@ -0,0 +1,28 @@ + + + $out_file1 && + echo "startCol $input1.metadata.startCol" >> $out_file1 && + echo "endCol $input1.metadata.endCol" >> $out_file1 && + echo "strandCol $input1.metadata.strandCol" >> $out_file1 + ]]> + + + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml index 2d6d3602f68..00e29ea8da5 100644 --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -59,6 +59,7 @@ +