add explicit gbk suffix (#6223)

galaxyproject · Aug 11, 2024 · 8a0f309 · 8a0f309
1 parent 49a2861
commit 8a0f309
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Showing 2 changed files with 2,832 additions and 3 deletions.
diff --git a/tools/bigscape/bigscape.xml b/tools/bigscape/bigscape.xml
@@ -2,7 +2,7 @@
     <description>Construct sequence similarity networks of BGCs and group them into GCF</description>
     <macros>
         <token name="@TOOL_VERSION@">1.1.9</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">BiG-SCAPE</xref>
@@ -17,7 +17,7 @@
         mkdir -p '$path_to_html' result input &&
         #for $files in $inputdir:
             #set $filename = "region." + $files.element_identifier
-            ln -s '$files' './input/$filename' &&
+            ln -s '$files' './input/${filename}.gbk' &&
         #end for
 
         mkdir pfam && 
@@ -296,7 +296,13 @@
         </test>
         <test expect_num_outputs="5">
             <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
-            <param name="inputdir" value="NC_010530.1.region005.gbk,NC_012963.1.region001.gbk,NW_009799099.1.region003.gbk,NW_021940918.1.region003.gbk,NW_009799102.1.region001.gbk,NW_022985561.1.region002.gbk,NW_022985549.1.region005.gbk,NW_022985575.1.region001.gbk" ftype="genbank" />
+            <param name="inputdir" value="NC_012963.1.region001.no-genbank-suffix,NC_010530.1.region005.gbk,NC_012963.1.region001.gbk,NW_009799099.1.region003.gbk,NW_021940918.1.region003.gbk,NW_009799102.1.region001.gbk,NW_022985561.1.region002.gbk,NW_022985549.1.region005.gbk,NW_022985575.1.region001.gbk" ftype="genbank" />
+            <param name="log" value="true" />
+            <param name="clans_off" value="true" />
+        </test>
+        <test expect_num_outputs="5">
+            <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
+            <param name="inputdir" value="NC_012963.1.region001.no-genbank-suffix,NC_010530.1.region005.gbk" ftype="genbank" />
             <param name="log" value="true" />
             <param name="clans_off" value="true" />
         </test>