Unverified Commit 50bdd355 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #14513 from bernt-matthias/topic/bed-metadata 

[21.01] fix metadata setting for bed and interval
parents 2d535ed9 9b66e46a

lib/galaxy/datatypes/interval.py

+4 −4
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
@@ -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):

test/functional/tools/metadata_bed.xml

0 → 100644
+28 −0
Original line number Diff line number Diff line 
<tool id="metadata_bed" name="BED metadata test" version="1.0.0">

    <command>

    <![CDATA[

    echo "chromCol $input1.metadata.chromCol" > $out_file1 &&

    echo "startCol $input1.metadata.startCol" >> $out_file1 &&

    echo "endCol $input1.metadata.endCol" >> $out_file1 &&

    echo "strandCol $input1.metadata.strandCol" >> $out_file1

    ]]>

    </command>

    <inputs>

        <param format="interval" name="input1" type="data" label="Choose intervals"/>

    </inputs>

    <outputs>

        <data format="txt" name="out_file1"/>

    </outputs>

    <tests>

        <test>

            <param name="input1" value="1.bed" ftype="bed"/>

            <output name="out_file1">

                <assert_contents>

                    <has_text text="strandCol 6"/>

                </assert_contents>

            </output>

        </test>

    </tests>

    <help>

    </help>

</tool>

test/functional/tools/samples_tool_conf.xml

+1 −0
Original line number Diff line number Diff line
@@ -57,6 +57,7 @@ 
  <tool file="metadata.xml" />

  <tool file="metadata_bam.xml" />

  <tool file="metadata_bcf.xml" />

  <tool file="metadata_bed.xml" />

  <tool file="metadata_biom1.xml" />

  <tool file="metadata_column_names.xml" />

  <tool file="strict_shell.xml" />