Bug fix: update all_fasta columns in clair3 repo (galaxyproject#6311)

* Give all_fasta four columns in clair3 tool_data_table entry * bump version suffix
bernt-matthias · Sep 9, 2024 · 79c3c11 · 79c3c11
1 parent 84328e6
commit 79c3c11
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Showing 5 changed files with 7 additions and 7 deletions.
diff --git a/tools/clair3/clair3.xml b/tools/clair3/clair3.xml
@@ -2,7 +2,7 @@
     <description>germline small variant caller for long-reads</description>
     <macros>
         <token name="@TOOL_VERSION@">1.0.8</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <xrefs>
         <xref type='bio.tools'>clair3</xref>

diff --git a/tools/clair3/test-data/all_fasta.loc b/tools/clair3/test-data/all_fasta.loc
@@ -4,7 +4,7 @@
 #all_fasta.loc. This file has the format (white space characters are
 #TAB characters):
 #
-#<unique_build_id>	<display_name>	<file_path>
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
 #
 #So, all_fasta.loc could look something like this:
-test1	"Test Genome"	${__HERE__}/test1.fasta
+test1	test1	"Test Genome"	${__HERE__}/test1.fasta
diff --git a/tools/clair3/tool-data/all_fasta.loc.sample b/tools/clair3/tool-data/all_fasta.loc.sample
@@ -4,7 +4,7 @@
 #all_fasta.loc. This file has the format (white space characters are
 #TAB characters):
 #
-#<unique_build_id>	<display_name>	<file_path>
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
 #
 #So, all_fasta.loc could look something like this:
-#test1	Test-Genome	./test-data/test1.fa
+#test1	test1	Test-Genome	./test-data/test1.fa
diff --git a/tools/clair3/tool_data_table_conf.xml.sample b/tools/clair3/tool_data_table_conf.xml.sample
@@ -6,7 +6,7 @@
         <file path="tool-data/model.loc" />
     </table>
     <table name="all_fasta" comment_char="#">
-        <columns>value, name, path</columns>
+        <columns>value, dbkey, name, path</columns>
         <file path="tool-data/all_fasta.loc" />
     </table>
 </tables>
diff --git a/tools/clair3/tool_data_table_conf.xml.test b/tools/clair3/tool_data_table_conf.xml.test
@@ -7,7 +7,7 @@
     </table>
     <!-- Locations of reference genome files in fasta format -->
     <table name="all_fasta" comment_char="#">
-        <columns>value, name, path</columns>
+        <columns>value, dbkey, name, path</columns>
         <file path="${__HERE__}/test-data/all_fasta.loc" />
     </table>
 </tables>