Adjust behavior of command_input_file_expression (#128)

Changes it to reference another input parameter instead of using self.
The behavior of processing secondary files patterns in order and being
able to reference earlier ones later is not part of the spec.

This doesn't exactly replicate the previous behavior, because it
introduces a new input parameter, however it does demonstrate the
ability to rename a file and have it staged as a secondary file
without having to use InitialWorkDir.

refs #127

Co-authored-by: Michael R. Crusoe <[email protected]>

Author: tetron

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)

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

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