Add test that changing basename with an ExpressionTool (#158)

Test to assert that when used in a command line tool it does actually
use the specified basename and not the original file name.

Author: tetron

conformance_tests.yaml

@@ -3469,7 +3469,7 @@
   tags: [ required, command_line_tool ]
 
 - label: record_with_default
-  output: 
+  output:
     same_record:
         first: y
         second: 23
@@ -3514,3 +3514,11 @@
   tool: tests/record_outputeval_nojs.cwl
   doc: Use of outputEval on a record itself, not the fields of the record (without javascript)
   tags: [ required, command_line_tool ]
+
+- label: staging-basename
+  output: {}
+  tool: tests/staging-basename/wf_ren.cwl
+  doc: |
+    Use of expression tool to change basename of file, then correctly staging
+    the file using the new name.
+  tags: [ required, command_line_tool, inline_javascript, expression_tool ]

tests/staging-basename/check.cwl

@@ -0,0 +1,18 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  p: File
+  checkname: string
+outputs: []
+arguments:
+  - sh
+  - "-c"
+  - |
+    name=`basename $(inputs.p.path)`
+    ls -l $(inputs.p.path)
+    if test $name = $(inputs.checkname) ; then
+      echo success
+    else
+      echo expected basename to be $(inputs.checkname) but was $name
+      exit 1
+    fi

tests/staging-basename/rename.cwl

@@ -0,0 +1,12 @@
+class: ExpressionTool
+cwlVersion: v1.2
+inputs:
+  f1: File
+  newname: string
+outputs:
+  out: File
+expression: |
+  ${
+  inputs.f1.basename = inputs.newname;
+  return {"out": inputs.f1};
+  }

tests/staging-basename/wf_ren.cwl

@@ -0,0 +1,29 @@
+class: Workflow
+cwlVersion: v1.2
+inputs:
+  f1:
+    type: File
+    default:
+      class: File
+      location: whale.txt
+  newname:
+    type: string
+    default:  "badger.txt"
+outputs: []
+requirements:
+  StepInputExpressionRequirement: {}
+  InlineJavascriptRequirement: {}
+steps:
+  rename:
+    in:
+      f1: f1
+      newname: newname
+    run: rename.cwl
+    out: [out]
+
+  echo:
+    in:
+      p: rename/out
+      checkname: newname
+    out: []
+    run: check.cwl

tests/staging-basename/whale.txt

@@ -0,0 +1 @@
+whale