Merge pull request #18357 from bernt-matthias/sift-fix

Fix loading error for built in tool `sift`
galaxyproject · Jun 10, 2024 · 81a00cb · 81a00cb
2 parents c42c349 + 654c702
commit 81a00cb
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/lib/galaxy/config/sample/tool_data_table_conf.xml.sample b/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
@@ -110,6 +110,10 @@
         <columns>value, name, url</columns>
         <file path="tool-data/icn3d_simple_display.loc" />
     </table>
+    <table name="sift_db" comment_char="#" allow_duplicate_entries="False">
+        <columns>dbkey, value</columns>
+        <file path="tool-data/sift_db.loc" />
+    </table>
     <!-- Refgenie __dbkeys__ -->
     <table name="__dbkeys__" type="refgenie" asset="fasta" >
         <file from_config="refgenie_config_file" />

diff --git a/tools/phenotype_association/sift.xml b/tools/phenotype_association/sift.xml
@@ -8,7 +8,7 @@
   <inputs>
     <param name="input" type="data" format="tabular" label="Dataset">
       <validator type="unspecified_build"/>
-      <validator type="dataset_metadata_in_file" filename="sift_db.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build."/>
+      <validator type="dataset_metadata_in_data_table" table_name="sift_db" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build."/>
     </param>
     <param name="chrom_col"  type="data_column" data_ref="input" label="Column with chromosome"/>
     <param name="pos_col"    type="data_column" data_ref="input" numerical="true" label="Column with position"/>