Commit fe303085 authored by Matthias Bernt's avatar Matthias Bernt
Browse files

bed, interval: set default for strandCol 

bed and interval datatypes `check element_is_set` before overwriting
metadata. since the having `default=None` and `no_value=0` makes
`element_is_set` return True (since `None!=0`). Therefore metadata
values are never set
parent 4e23fbb0

lib/galaxy/datatypes/interval.py

+2 −2
Original line number Diff line number Diff line
@@ -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