Unverified Commit 70b2ea42 authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Merge branch 'release_22.01' into release_22.05

parents 2b450df9 9f1d8d05

lib/galaxy/datatypes/interval.py

+4 −0
Original line number Diff line number Diff line
@@ -86,6 +86,7 @@ class Interval(Tabular): 
    MetadataElement(name="endCol", default=3, desc="End column", param=metadata.ColumnParameter)

    MetadataElement(

        name="strandCol",

        default=0,

        desc="Strand column (click box & select)",

        param=metadata.ColumnParameter,

        optional=True,
@@ -459,6 +460,7 @@ class Bed(Interval): 
    MetadataElement(name="endCol", default=3, desc="End column", param=metadata.ColumnParameter)

    MetadataElement(

        name="strandCol",

        default=0,

        desc="Strand column (click box & select)",

        param=metadata.ColumnParameter,

        optional=True,
@@ -687,6 +689,7 @@ class BedStrict(Bed): 
    MetadataElement(name="endCol", default=3, desc="End column", readonly=True, param=metadata.MetadataParameter)

    MetadataElement(

        name="strandCol",

        default=0,

        desc="Strand column (click box & select)",

        readonly=True,

        param=metadata.MetadataParameter,
@@ -1613,6 +1616,7 @@ class ENCODEPeak(Interval): 
    MetadataElement(name="endCol", default=3, desc="End column", param=metadata.ColumnParameter)

    MetadataElement(

        name="strandCol",

        default=0,

        desc="Strand column (click box & select)",

        param=metadata.ColumnParameter,

        optional=True,

lib/galaxy/tools/__init__.py

+1 −1
Original line number Diff line number Diff line
@@ -1190,7 +1190,7 @@ class Tool(Dictifiable): 
        if getattr(self, "tool_shed", None):

            tool_dir = Path(self.tool_dir)

            for repo_dir in itertools.chain([tool_dir], tool_dir.parents):

                if repo_dir.name == self.repository_name:

                if repo_dir.name == self.repository_name and repo_dir.parent.name == self.installed_changeset_revision:

                    return str(repo_dir)

            else:

                log.error(f"Problem finding repository dir for tool '{self.id}'")

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
@@ -67,6 +67,7 @@ 
  <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" />