Merge pull request #6357 from bernt-matthias/lint-arriba

arriba fix validator
galaxyproject · Sep 25, 2024 · 26aa67f · 26aa67f
2 parents 544fd49 + 6dcaf0c
commit 26aa67f
Show file tree

Hide file tree

Showing 3 changed files with 2 additions and 3 deletions.
diff --git a/tools/arriba/.lint_skip b/tools/arriba/.lint_skip
diff --git a/tools/arriba/arriba.xml b/tools/arriba/arriba.xml
@@ -217,7 +217,7 @@
                       Asterisks (*) are treated as wild-cards.
                       Default: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*
                 </help>
-                <validator type="regex" message="not a valid contig name">^((@GENOME_CONTIG@|@VIRAL_CONTIG@)([,\s]\s*(*@GENOME_CONTIG@|@VIRAL_CONTIG@))*)*</validator>
+                <validator type="regex" message="not a valid contig name">^((@GENOME_CONTIG@|@VIRAL_CONTIG@)([,\s]\s*(@GENOME_CONTIG@|@VIRAL_CONTIG@))*)$</validator>
             </param>
             <param name="viral_contigs" argument="-v" type="text" value="" optional="true" label="Comma/space-separated list of viral contigs">
                 <help>Comma-/space-separated list of viral contigs for reporting of viral integration sites. 

diff --git a/tools/arriba/macros.xml b/tools/arriba/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.4.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>