Merge branch 'release_22.01' into release_22.05

lib/galaxy/datatypes/interval.py

@@ -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

@@ -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

@@ -0,0 +1,28 @@
+<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

@@ -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" />