$5 in the baseCommand nor the arguments list should be evaluated

v1.0/conformance_test_v1.0.yaml

@@ -1593,3 +1593,25 @@
     inputs are not present in the input object used to run the tool.
   should_fail: true
   tags: [ required ]
+
+- tool: v1.0/awk-awk.cwl
+  job: v1.0/awk-awk-job.yaml
+  doc: test that a $ in the baseCommand is not interpreted by the shell
+  output:
+    bRegionsNonZero:
+        basename: awk-awk-input_nonZero.txt
+        class: File
+        checksum: "sha1$810037850eb6f1791e9365e25f124808828070e2"
+        size: 24
+  tags: [ required ]
+
+- tool: v1.0/awk-awk2.cwl
+  job: v1.0/awk-awk-job.yaml
+  doc: test that a $ in an argument is not interpreted by the shell
+  output:
+    bRegionsNonZero:
+        basename: awk-awk-input_nonZero.txt
+        class: File
+        checksum: "sha1$810037850eb6f1791e9365e25f124808828070e2"
+        size: 24
+  tags: [ required ]

v1.0/v1.0/awk-awk-input

@@ -0,0 +1,2 @@
+this will be ignored 0
+this will be selected 1

v1.0/v1.0/awk-awk-job.yaml

@@ -0,0 +1,3 @@
+atoBComparison:
+  class: File
+  path: awk-awk-input

v1.0/v1.0/awk-awk.cwl

@@ -0,0 +1,13 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  atoBComparison:
+    type: File
+    inputBinding:
+      position: 1
+outputs:
+  bRegionsNonZero:
+    type: stdout
+stdout: $(inputs.atoBComparison.basename)_nonZero.txt
+baseCommand: [awk, "$5!=0"]

v1.0/v1.0/awk-awk2.cwl

@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+inputs:
+  atoBComparison:
+    type: File
+    inputBinding:
+      position: 1
+outputs:
+  bRegionsNonZero:
+    type: stdout
+stdout: $(inputs.atoBComparison.basename)_nonZero.txt
+baseCommand: awk
+arguments: ["$5!=0"]