add additional examples

from https://github.com/common-workflow-language/cwl-v1.2/tree/e15d7b77ceecc503382561d04eaf1fc140d80f12/tests

Author: mr-c

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

@@ -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

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

@@ -0,0 +1,16 @@
+class: CommandLineTool
+cwlVersion: v1.2
+baseCommand: "true"
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: $(inputs.newname)
+        entry: $(inputs.srcfile)
+inputs:
+  srcfile: File
+  newname: string
+outputs:
+  outfile:
+    type: File
+    outputBinding:
+      glob: $(inputs.newname)

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

@@ -0,0 +1,26 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.2
+
+requirements:
+  - class: InlineJavascriptRequirement
+  - class: SchemaDefRequirement
+    types:
+      - $import: schemadef_types_with_import_readgroup.yml
+
+inputs:
+    - id: message
+      type: "schemadef_types_with_import_readgroup.yml#readgroups_bam_file"
+      inputBinding:
+        valueFrom: $(self.readgroup_meta_list[0]['DT'])
+
+outputs:
+    - id: out
+      type: string
+      outputBinding:
+        glob: output.txt
+        loadContents: true
+        outputEval: $(self[0].contents)
+
+stdout: output.txt
+baseCommand: echo

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

@@ -0,0 +1,27 @@
+- name: readgroup_meta
+  type: record
+  fields:
+    - name: CN
+      type: string
+    - name: DT
+      type: string
+    - name: ID
+      type: string
+    - name: LB
+      type: string
+    - name: PI
+      type: string
+    - name: PL
+      type: string
+    - name: SM
+      type: string
+
+- name: readgroups_bam_file
+  type: record
+  fields:
+    - name: bam
+      type: File
+    - name: readgroup_meta_list
+      type:
+        type: array
+        items: readgroup_meta

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

@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.2
+inputs:
+  dir1:
+    type: Directory
+    inputBinding:
+      valueFrom: $(self.listing[0].listing[0].path)
+outputs:
+  output_file:
+    type: File
+    outputBinding: {glob: output.txt}
+baseCommand: cat
+stdout: output.txt

src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_cat4-from-dir.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

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

@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.2
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/bash:4.4
+inputs:
+  input_file: File
+  outdir_name: string
+
+baseCommand: [ bash, -c ]
+stdout: re:sult
+arguments:
+ - |
+   mkdir $(inputs.outdir_name);
+   cp $(inputs.input_file.path) $(inputs.outdir_name)/;
+   echo Status: done!
+outputs:
+  log: stdout
+  result:
+    type: Directory
+    outputBinding:
+      glob: $(inputs.outdir_name)

src/test/resources/org/w3id/cwl/cwl1_2/utils/valid_colon:test.cwl

@@ -0,0 +1,20 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.2
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/bash:4.4
+inputs:
+  input_file: File
+  outdir_name: string
+
+baseCommand: [ bash, -c ]
+arguments:
+ - |
+   mkdir $(inputs.outdir_name);
+   cp $(inputs.input_file.path) $(inputs.outdir_name)/;
+outputs:
+  result:
+    type: Directory
+    outputBinding:
+      glob: $(inputs.outdir_name)

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

@@ -0,0 +1,33 @@
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+requirements:
+  - class: InlineJavascriptRequirement
+
+baseCommand: ['echo']
+
+inputs:
+  message:
+    type:
+      type: record
+      name: message_object
+      fields:
+        text:
+          type: string
+          inputBinding:
+            position: 1
+        newlines:
+          type: boolean?
+          inputBinding:
+            position: 0
+            prefix: -n
+
+outputs:
+  out:
+    type: string
+    outputBinding:
+      glob: output.txt
+      loadContents: true
+      outputEval: $(self[0].contents)
+stdout: output.txt