From 75c59146721b93478fc17ae0f2f5e5487e315b3b Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 28 May 2018 01:42:04 -0700
Subject: [PATCH 1/2] Multi item baseCommand quoting test

---
 v1.0/conformance_test_v1.0.yaml | 11 +++++++++++
 v1.0/v1.0/awk-awk-input         |  2 ++
 v1.0/v1.0/awk-awk-job.yaml      |  3 +++
 v1.0/v1.0/awk-awk.cwl           | 13 +++++++++++++
 4 files changed, 29 insertions(+)
 create mode 100644 v1.0/v1.0/awk-awk-input
 create mode 100644 v1.0/v1.0/awk-awk-job.yaml
 create mode 100644 v1.0/v1.0/awk-awk.cwl

diff --git a/v1.0/conformance_test_v1.0.yaml b/v1.0/conformance_test_v1.0.yaml
index 1c871cc9..9b175d02 100644
--- a/v1.0/conformance_test_v1.0.yaml
+++ b/v1.0/conformance_test_v1.0.yaml
@@ -1593,3 +1593,14 @@
     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 quoting with multi-entry baseCommand
+  output:
+    bRegionsNonZero:
+        basename: awk-awk-input_nonZero.txt
+        class: File
+        checksum: "sha1$810037850eb6f1791e9365e25f124808828070e2"
+        size: 24
+  tags: [ required ]
diff --git a/v1.0/v1.0/awk-awk-input b/v1.0/v1.0/awk-awk-input
new file mode 100644
index 00000000..7c16ebf2
--- /dev/null
+++ b/v1.0/v1.0/awk-awk-input
@@ -0,0 +1,2 @@
+this will be ignored 0
+this will be selected 1
diff --git a/v1.0/v1.0/awk-awk-job.yaml b/v1.0/v1.0/awk-awk-job.yaml
new file mode 100644
index 00000000..c1fdd51d
--- /dev/null
+++ b/v1.0/v1.0/awk-awk-job.yaml
@@ -0,0 +1,3 @@
+atoBComparison:
+  class: File
+  path: awk-awk-input
diff --git a/v1.0/v1.0/awk-awk.cwl b/v1.0/v1.0/awk-awk.cwl
new file mode 100644
index 00000000..860a8b20
--- /dev/null
+++ b/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"]

From 128a460935af67af415faf37cb5921c1d16976a4 Mon Sep 17 00:00:00 2001
From: "Michael R. Crusoe" <michael.crusoe@gmail.com>
Date: Mon, 28 May 2018 02:14:38 -0700
Subject: [PATCH 2/2] clarify and expand

---
 v1.0/conformance_test_v1.0.yaml | 13 ++++++++++++-
 v1.0/v1.0/awk-awk2.cwl          | 14 ++++++++++++++
 2 files changed, 26 insertions(+), 1 deletion(-)
 create mode 100644 v1.0/v1.0/awk-awk2.cwl

diff --git a/v1.0/conformance_test_v1.0.yaml b/v1.0/conformance_test_v1.0.yaml
index 9b175d02..7e9742c8 100644
--- a/v1.0/conformance_test_v1.0.yaml
+++ b/v1.0/conformance_test_v1.0.yaml
@@ -1596,7 +1596,18 @@
 
 - tool: v1.0/awk-awk.cwl
   job: v1.0/awk-awk-job.yaml
-  doc: test quoting with multi-entry baseCommand
+  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
diff --git a/v1.0/v1.0/awk-awk2.cwl b/v1.0/v1.0/awk-awk2.cwl
new file mode 100644
index 00000000..06660b11
--- /dev/null
+++ b/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"]