add tests: 91 failures

Author: mr-c

src/test/java/org/w3id/cwl/cwl1_2/utils/ExamplesTest.java

@@ -0,0 +1,10 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  initial_file: File
+  out_file_name: string
+outputs:
+  processed_file: stdout
+stdout: $(inputs.out_file_name)
+arguments: [echo, $(inputs.initial_file.basename)]

src/test/resources/org/w3id/cwl/cwl1_2/utils/EDAM.owl

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+import sys
+import json
+import os
+args = [os.path.basename(a) for a in sys.argv[1:]]
+with open("cwl.output.json", "w") as f:
+    json.dump({"args": args}, f)

src/test/resources/org/w3id/cwl/cwl1_2/utils/action.cwl

@@ -0,0 +1,10 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  in1: int
+baseCommand: [echo]
+outputs:
+  out1:
+    type: string
+    outputBinding:
+      outputEval: bar $(inputs.in1)

src/test/resources/org/w3id/cwl/cwl1_2/utils/args.py

@@ -0,0 +1,5 @@
+- name: capture_kit
+  type: record
+  fields:
+    - name: bait
+      type: string

src/test/resources/org/w3id/cwl/cwl1_2/utils/bar.cwl

@@ -0,0 +1,17 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.2
+
+inputs:
+  file1: File
+
+outputs:
+  output:
+    type: File
+    outputBinding: { glob: output }
+
+baseCommand: [cat]
+
+stdin: $(inputs.file1.path)
+stdout: output

src/test/resources/org/w3id/cwl/cwl1_2/utils/capture_kit.yml

@@ -0,0 +1,12 @@
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  in1: int
+  in2: int
+  in3: int
+baseCommand: [echo]
+outputs:
+  out1:
+    type: string
+    outputBinding:
+      outputEval: $(inputs.in1)$(inputs.in2)$(inputs.in3)

src/test/resources/org/w3id/cwl/cwl1_2/utils/cat-tool.cwl

@@ -0,0 +1,19 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.2
+
+inputs:
+  file1:
+    type: File
+
+outputs:
+  wc_output:
+    type: File
+    outputSource: step1/output
+
+steps:
+  step1:
+    run: wc-tool.cwl
+    in:
+      file1: file1
+    out: [output]

src/test/resources/org/w3id/cwl/cwl1_2/utils/cat.cwl

@@ -0,0 +1,25 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.2
+
+inputs:
+  file1:
+    type: File
+
+outputs:
+  count_output:
+    type: int
+    outputSource: step2/output
+
+steps:
+  step1:
+    run: wc-tool.cwl
+    in:
+      file1: file1
+    out: [output]
+
+  step2:
+    run: parseInt-tool.cwl
+    in:
+      file1: step1/output
+    out: [output]