diff --git a/tests/secondaryfiles/rename-inputs.cwl b/tests/secondaryfiles/rename-inputs.cwl
index bffc0311..484c3f58 100644
--- a/tests/secondaryfiles/rename-inputs.cwl
+++ b/tests/secondaryfiles/rename-inputs.cwl
@@ -1,7 +1,5 @@
 #!/usr/bin/env cwl-runner
 id: InputSecondaryFileConformanceTest
-baseCommand:
-- ls
 class: CommandLineTool
 cwlVersion: v1.2
 doc: |
@@ -24,7 +22,6 @@ inputs:
     touch secondary_file_test.txt.accessory
     ```
   secondaryFiles:
-    - .accessory
     - |
       ${
         function resolveSecondary(base, secPattern) {
@@ -37,19 +34,21 @@ inputs:
         }
         return [{
             "class": "File",
-            "location": self.secondaryFiles[0].location,
+            "location": inputs.accessory.location,
             "basename": resolveSecondary(self.basename, '^.accessory')
         }];
       }
+- id: accessory
+  type: File
+
 
 arguments:
+- "ls"
+- $(inputs.inputWithSecondary.dirname)
 - valueFrom: "|"
   shellQuote: false
-  position: 0
-- valueFrom: "grep"
-  position: 1
-- valueFrom: "secondary"
-  position: 2
+- "grep"
+- "secondary"
 
 outputs:
 - id: output_file
@@ -58,6 +57,3 @@ stdout: result
 requirements:
   InlineJavascriptRequirement: {}
   ShellCommandRequirement: {}
-  InitialWorkDirRequirement:
-    listing:
-    - $(inputs.inputWithSecondary)
diff --git a/tests/secondaryfiles/rename-inputs.yml b/tests/secondaryfiles/rename-inputs.yml
index de72eec9..90393b72 100644
--- a/tests/secondaryfiles/rename-inputs.yml
+++ b/tests/secondaryfiles/rename-inputs.yml
@@ -1,3 +1,6 @@
 inputWithSecondary:
     class: File
     location: secondary_file_test.txt
+accessory:
+    class: File
+    location: secondary_file_test.txt.accessory
diff --git a/tests/secondaryfiles/test-index.yaml b/tests/secondaryfiles/test-index.yaml
index 79fae852..6ecec1d6 100644
--- a/tests/secondaryfiles/test-index.yaml
+++ b/tests/secondaryfiles/test-index.yaml
@@ -8,7 +8,7 @@
       checksum: sha1$901c3d387a263c57eaed6f24a82517c1fb0e198d
       size: 54
       location: result
-  tags: [ inline_javascript, secondary_files, command_line_tool ]
+  tags: [ inline_javascript, secondary_files, command_line_tool, shell_command ]
 
 - tool: rename-outputs.cwl
   doc: Confirm CommandOutputParameter expression can receive a File object