Merge pull request galaxyproject#5461 from pimarin/bakta

Update bakta from 1.8.1 to 1.8.2
Delphine-L · Sep 16, 2023 · 5ab9313 · 5ab9313
2 parents 66e797a + 2ed1885
commit 5ab9313
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diff --git a/tools/bakta/bakta.xml b/tools/bakta/bakta.xml
diff --git a/tools/bakta/macro.xml b/tools/bakta/macro.xml
@@ -1,8 +1,8 @@
 
 <macros>
-    <token name="@TOOL_VERSION@">1.8.1</token>
+    <token name="@TOOL_VERSION@">1.8.2</token>
     <token name="@COMPATIBLE_BAKTA_VERSION@">1.7</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="version_command">
         <version_command><![CDATA[bakta --version]]></version_command>
@@ -27,4 +27,15 @@
             <citation type="doi">10.1099/mgen.0.000685</citation>
         </citations>
     </xml>
+
+    <xml name="assert_content_test">
+        <assert_contents>
+            <has_text text="Options and arguments"/>
+            <has_text text="parse genome sequences"/>
+            <has_text text="start annotation"/>
+            <has_text text="genome statistics"/>
+            <has_text text="annotation summary"/>
+            <has_text text="export annotation results to"/>
+         </assert_contents>    
+    </xml>
 </macros>
diff --git a/tools/bakta/test-data/TEST_1/TEST_1.gff3 b/tools/bakta/test-data/TEST_1/TEST_1.gff3
@@ -1,7 +1,7 @@
 ##gff-version 3
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta

diff --git a/tools/bakta/test-data/TEST_1/TEST_1.hypotheticals.tsv b/tools/bakta/test-data/TEST_1/TEST_1.hypotheticals.tsv
@@ -1,4 +1,4 @@
-#Annotated with Bakta v1.8.1, https://github.com/oschwengers/bakta
+#Annotated with Bakta v1.8.2, https://github.com/oschwengers/bakta
 #Database v5.0, https://doi.org/10.5281/zenodo.4247252
 #Sequence Id	Start	Stop	Strand	Locus Tag	Mol Weight [kDa]	Iso El. Point	Pfam hits	Dbxrefs
 contig_1	413	736	+	IHHALP_00005	12.1	10.4		

diff --git a/tools/bakta/test-data/TEST_1/TEST_1.log b/tools/bakta/test-data/TEST_1/TEST_1.log
diff --git a/tools/bakta/test-data/TEST_1/TEST_1.tsv b/tools/bakta/test-data/TEST_1/TEST_1.tsv
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta

diff --git a/tools/bakta/test-data/TEST_1/TEST_1.txt b/tools/bakta/test-data/TEST_1/TEST_1.txt
@@ -24,7 +24,7 @@ oriVs: 0
 oriTs: 0
 
 Bakta:
-Software: v1.8.1
+Software: v1.8.2
 Database: v5.0, full
 DOI: 10.1099/mgen.0.000685
 URL: github.com/oschwengers/bakta
diff --git a/tools/bakta/test-data/TEST_2/TEST_2.gff3 b/tools/bakta/test-data/TEST_2/TEST_2.gff3
@@ -2,7 +2,7 @@
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # organism Escherichia coli o157:h7 Sakai
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta

diff --git a/tools/bakta/test-data/TEST_2/TEST_2.tsv b/tools/bakta/test-data/TEST_2/TEST_2.tsv
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta

diff --git a/tools/bakta/test-data/TEST_3/TEST_3.gff3 b/tools/bakta/test-data/TEST_3/TEST_3.gff3
@@ -1,7 +1,7 @@
 ##gff-version 3
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta

diff --git a/tools/bakta/test-data/TEST_3/TEST_3.tsv b/tools/bakta/test-data/TEST_3/TEST_3.tsv
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta

diff --git a/tools/bakta/test-data/TEST_4/TEST_4.gff3 b/tools/bakta/test-data/TEST_4/TEST_4.gff3
@@ -1,7 +1,7 @@
 ##gff-version 3
 ##feature-ontology https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/v3.1/so.obo
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta

diff --git a/tools/bakta/test-data/TEST_4/TEST_4.tsv b/tools/bakta/test-data/TEST_4/TEST_4.tsv
@@ -1,5 +1,5 @@
 # Annotated with Bakta
-# Software: v1.8.1
+# Software: v1.8.2
 # Database: v5.0, full
 # DOI: 10.1099/mgen.0.000685
 # URL: github.com/oschwengers/bakta

diff --git a/tools/bakta/test-data/TEST_5/TEST_5.log b/tools/bakta/test-data/TEST_5/TEST_5.log
diff --git a/tools/bakta/test-data/TEST_5/TEST_5.txt b/tools/bakta/test-data/TEST_5/TEST_5.txt
@@ -24,7 +24,7 @@ oriVs: 0
 oriTs: 0
 
 Bakta:
-Software: v1.8.1
+Software: v1.8.2
 Database: v5.0, full
 DOI: 10.1099/mgen.0.000685
 URL: github.com/oschwengers/bakta