Change input binding to arguments in example files

src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl

@@ -11,7 +11,7 @@ arguments: ["-d", $(runtime.outdir)]
 inputs:
   src:
     type: File
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   classfile:

src/_includes/cwl/custom-types/custom-types.cwl

@@ -24,11 +24,11 @@ inputs:
   biom:
     type: File
     format: edam:format_3746  # BIOM
-    inputBinding:
+    arguments:
       prefix: --input-fp
   table_type:
     type: biom-convert-table.yaml#table_type
-    inputBinding:
+    arguments:
       prefix: --table-type
 
   header_key:
@@ -37,7 +37,7 @@ inputs:
       The observation metadata to include from the input BIOM table file when
       creating a tsv table file. By default no observation metadata will be
       included.
-    inputBinding:
+    arguments:
       prefix: --header-key
 
 baseCommand: [ biom, convert ]

src/_includes/cwl/echo.cwl

@@ -8,7 +8,7 @@ stdout: output.txt
 inputs:
   message:
     type: string
-    inputBinding: {}
+    arguments: {}
 outputs:
   out:
     type: string

src/_includes/cwl/file-formats/metadata_example.cwl

@@ -9,7 +9,7 @@ inputs:
     type: File
     label: Aligned sequences in BAM format
     format: edam:format_2572
-    inputBinding:
+    arguments:
       position: 1
 
 baseCommand: [ wc, -l ]

src/_includes/cwl/hello_world.cwl

@@ -12,6 +12,6 @@ inputs:
     # A default value that can be overridden, e.g. --message "Hola mundo"
     default: "Hello World"
     # Bind this message value as an argument to "echo".
-    inputBinding:
+    arguments:
       position: 1
 outputs: []

src/_includes/cwl/inputs/array-inputs.cwl

@@ -5,23 +5,23 @@ class: CommandLineTool
 inputs:
   filesA:
     type: string[]
-    inputBinding:
+    arguments:
       prefix: -A
       position: 1
 
   filesB:
     type:
       type: array
       items: string
-      inputBinding:
+      arguments:
         prefix: -B=
         separate: false
-    inputBinding:
+    arguments:
       position: 2
 
   filesC:
     type: string[]
-    inputBinding:
+    arguments:
       prefix: -C=
       itemSeparator: ","
       separate: false

src/_includes/cwl/inputs/exclusive-parameter-expressions.cwl

@@ -13,7 +13,7 @@ inputs:
           - fastq
           - fasta.gz
           - fastq.gz
-        inputBinding:
+        arguments:
           position: 0
           prefix: '--format'
 outputs:

src/_includes/cwl/inputs/inp.cwl

@@ -6,23 +6,23 @@ baseCommand: echo
 inputs:
   example_flag:
     type: boolean
-    inputBinding:
+    arguments:
       position: 1
       prefix: -f
   example_string:
     type: string
-    inputBinding:
+    arguments:
       position: 3
       prefix: --example-string
   example_int:
     type: int
-    inputBinding:
+    arguments:
       position: 2
       prefix: -i
       separate: false
   example_file:
     type: File?
-    inputBinding:
+    arguments:
       prefix: --file=
       separate: false
       position: 4

src/_includes/cwl/inputs/record.cwl

@@ -10,11 +10,11 @@ inputs:
       fields:
         itemA:
           type: string
-          inputBinding:
+          arguments:
             prefix: -A
         itemB:
           type: string
-          inputBinding:
+          arguments:
             prefix: -B
   exclusive_parameters:
     type:
@@ -23,14 +23,14 @@ inputs:
         fields:
           itemC:
             type: string
-            inputBinding:
+            arguments:
               prefix: -C
       - type: record
         name: itemD
         fields:
           itemD:
             type: string
-            inputBinding:
+            arguments:
               prefix: -D
 outputs:
   example_out:

src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl

@@ -10,7 +10,7 @@ inputs:
     type: File
     label: Aligned sequences in BAM format
     format: edam:format_2572
-    inputBinding:
+    arguments:
       position: 1
 
 baseCommand: [ wc, -l ]

src/_includes/cwl/operations/echo.cwl

@@ -12,6 +12,6 @@ inputs:
     # A default value that can be overridden, e.g. --message "Hola mundo"
     default: "Hello World"
     # Bind this message value as an argument to "echo".
-    inputBinding:
+    arguments:
       position: 1
 outputs: []

src/_includes/cwl/outputs/array-outputs.cwl

@@ -8,7 +8,7 @@ inputs:
     type:
       type: array
       items: string
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   output:

src/_includes/cwl/outputs/stdout.cwl

@@ -7,7 +7,7 @@ stdout: output.txt
 inputs:
   message:
     type: string
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   example_out:

src/_includes/cwl/outputs/tar.cwl

@@ -6,7 +6,7 @@ baseCommand: [tar, --extract]
 inputs:
   tarfile:
     type: File
-    inputBinding:
+    arguments:
       prefix: --file
 outputs:
   example_out:

src/_includes/cwl/parameter-references/tar-param.cwl

@@ -6,11 +6,11 @@ baseCommand: [tar, --extract]
 inputs:
   tarfile:
     type: File
-    inputBinding:
+    arguments:
       prefix: --file
   extractfile:
     type: string
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   extracted_file:

src/_includes/cwl/specifying-software-requirements/custom-types.cwl

@@ -28,11 +28,11 @@ hints:
 inputs:
   proteinFile:
     type: File
-    inputBinding:
+    arguments:
       prefix: --input
   applications:
     type: InterProScan-apps.yml#apps[]?
-    inputBinding:
+    arguments:
       itemSeparator: ','
       prefix: --applications
 

src/_includes/cwl/staging-input-files/linkfile.cwl

@@ -15,7 +15,7 @@ requirements:
 inputs:
   src:
     type: File
-    inputBinding:
+    arguments:
       position: 1
       valueFrom: $(self.basename)
 

src/_includes/cwl/using-containers/docker.cwl

@@ -9,7 +9,7 @@ hints:
 inputs:
   src:
     type: File
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   example_out:

src/_includes/cwl/workflows/arguments.cwl

@@ -11,7 +11,7 @@ arguments: ["-d", $(runtime.outdir)]
 inputs:
   src:
     type: File
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   classfile:

src/_includes/cwl/workflows/hello_world.cwl

@@ -6,7 +6,7 @@ baseCommand: echo
 inputs:
   message:
     type: string
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   echo_out:

src/_includes/cwl/workflows/hello_world_to_stdout.cwl

@@ -6,6 +6,6 @@ baseCommand: echo
 inputs:
   message:
     type: string
-    inputBinding:
+    arguments:
       position: 1
 outputs: []

src/_includes/cwl/workflows/tar-param.cwl

@@ -6,11 +6,11 @@ baseCommand: [tar, --extract]
 inputs:
   tarfile:
     type: File
-    inputBinding:
+    arguments:
       prefix: --file
   extractfile:
     type: string
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   extracted_file:

src/_includes/cwl/workflows/wc-tool.cwl

@@ -7,6 +7,6 @@ arguments: ["-c"]
 inputs:
   input_file:
     type: File
-    inputBinding:
+    arguments:
       position: 1
 outputs: []