omark: fix optional options (#5817)

galaxyproject · Mar 12, 2024 · 344924b · 344924b
1 parent 91a178d
commit 344924b
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Showing 2 changed files with 15 additions and 6 deletions.
diff --git a/tools/omark/macros.xml b/tools/omark/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.3.0</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
 
     <xml name="requirements">
         <requirement type="package" version="@TOOL_VERSION@">omark</requirement>

diff --git a/tools/omark/omark.xml b/tools/omark/omark.xml
@@ -17,11 +17,20 @@
     -f 'output_omamer'
     -d '$database.fields.path'
     $omark_mode
-    -i '$input_iso'
-    -t '$t'
-    -r '$r'
-    -o omark_galaxy
 
+    #if $input_iso:
+        -i '$input_iso'
+    #end if
+
+    #if $t:
+        -t '$t'
+    #end if
+
+    #if $r:
+        -r '$r'
+    #end if
+
+    -o omark_galaxy
     ]]></command>
 
     <inputs>
@@ -49,7 +58,7 @@
             <validator type="regex">[0-9a-zA-Z_]+</validator>
         </param>
 
-        <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
+        <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
             <option value="detail_sum" selected="true">Detailed summary</option>
             <option value="hog">HOG identifiers</option>
             <option value="pdf">PDF Graphic representation </option>