Merge branch 'release_21.05' into release_21.09

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):

lib/galaxy/tools/__init__.py

@@ -1147,7 +1147,7 @@ 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

@@ -64,6 +64,7 @@
   <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" />