From 97e919f33f6863ff826f65951d74efc35259a67d Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:19:40 +0100
Subject: [PATCH 01/23] Change inputBinding field to arguments

---
 .../cwl/additional-arguments-and-parameters/arguments.cwl       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl b/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl
index 3a2e4538..afc834dc 100644
--- a/src/_includes/cwl/additional-arguments-and-parameters/arguments.cwl
+++ b/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:

From 33beacd88f3c8dbbee9c51c4f25c8face9237ee4 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:29:21 +0100
Subject: [PATCH 02/23] change inputBinding field to arguments

---
 src/_includes/cwl/custom-types/custom-types.cwl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/_includes/cwl/custom-types/custom-types.cwl b/src/_includes/cwl/custom-types/custom-types.cwl
index 707d5c2a..8bdb6e9c 100644
--- a/src/_includes/cwl/custom-types/custom-types.cwl
+++ b/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 ]

From 4cf29cbd635452bebf8b5754d335229b630bce86 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:34:30 +0100
Subject: [PATCH 03/23] change inputBinding field to arguments

---
 src/_includes/cwl/file-formats/metadata_example.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/file-formats/metadata_example.cwl b/src/_includes/cwl/file-formats/metadata_example.cwl
index 9485522b..6b61f97a 100644
--- a/src/_includes/cwl/file-formats/metadata_example.cwl
+++ b/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 ]

From e337f112c25642e38ef38cb8f397b5e18463ac5c Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:36:52 +0100
Subject: [PATCH 04/23] change inputBinding field to arguments

---
 src/_includes/cwl/inputs/array-inputs.cwl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/_includes/cwl/inputs/array-inputs.cwl b/src/_includes/cwl/inputs/array-inputs.cwl
index bef63538..6ec6708e 100755
--- a/src/_includes/cwl/inputs/array-inputs.cwl
+++ b/src/_includes/cwl/inputs/array-inputs.cwl
@@ -5,7 +5,7 @@ class: CommandLineTool
 inputs:
   filesA:
     type: string[]
-    inputBinding:
+    arguments:
       prefix: -A
       position: 1
 
@@ -13,15 +13,15 @@ inputs:
     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

From ccea546f36e28327e36dcad4667e6616477ba6e6 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:37:53 +0100
Subject: [PATCH 05/23] change inputBinding field to arguments

---
 src/_includes/cwl/inputs/exclusive-parameter-expressions.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/inputs/exclusive-parameter-expressions.cwl b/src/_includes/cwl/inputs/exclusive-parameter-expressions.cwl
index dd98d0a5..0246b305 100644
--- a/src/_includes/cwl/inputs/exclusive-parameter-expressions.cwl
+++ b/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:

From d8b7667767da103132a7ddeb2a1987e8e69ad28b Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:39:02 +0100
Subject: [PATCH 06/23] change inputBinding field to arguments

---
 src/_includes/cwl/inputs/inp.cwl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/_includes/cwl/inputs/inp.cwl b/src/_includes/cwl/inputs/inp.cwl
index 576c16da..b90c886c 100755
--- a/src/_includes/cwl/inputs/inp.cwl
+++ b/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

From 988e6641cf605447a6bc5a70263bd2acb2a68670 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:40:38 +0100
Subject: [PATCH 07/23] change inputBinding field to arguments

---
 src/_includes/cwl/inputs/record.cwl | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/_includes/cwl/inputs/record.cwl b/src/_includes/cwl/inputs/record.cwl
index e33cb44a..737ea48e 100755
--- a/src/_includes/cwl/inputs/record.cwl
+++ b/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:

From 3e2a3b238a35c71dbcfdac6aee24c922c548a0ab Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:43:07 +0100
Subject: [PATCH 08/23] change inputBinding field to arguments

---
 src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl b/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl
index 745c1779..16b77120 100644
--- a/src/_includes/cwl/metadata-and-authorship/metadata_example2.cwl
+++ b/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 ]

From 80bcf0086758781fa354ca4a41630764bac87fce Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:43:49 +0100
Subject: [PATCH 09/23] change inputBinding field to arguments

---
 src/_includes/cwl/operations/echo.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/operations/echo.cwl b/src/_includes/cwl/operations/echo.cwl
index 3d35dbb8..4ac26fcd 100644
--- a/src/_includes/cwl/operations/echo.cwl
+++ b/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: []

From 1728d45dd9414fca88d117d51ac30895bb4d81c7 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:45:03 +0100
Subject: [PATCH 10/23] change inputBinding field to arguments

---
 src/_includes/cwl/outputs/array-outputs.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/outputs/array-outputs.cwl b/src/_includes/cwl/outputs/array-outputs.cwl
index 2d6654ea..571b3fba 100755
--- a/src/_includes/cwl/outputs/array-outputs.cwl
+++ b/src/_includes/cwl/outputs/array-outputs.cwl
@@ -8,7 +8,7 @@ inputs:
     type:
       type: array
       items: string
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   output:

From c81eb352c9d2167b11763ef351009a7972824614 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:46:06 +0100
Subject: [PATCH 11/23] change inputBinding field to arguments

---
 src/_includes/cwl/outputs/stdout.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/outputs/stdout.cwl b/src/_includes/cwl/outputs/stdout.cwl
index 5908f88f..ad984983 100755
--- a/src/_includes/cwl/outputs/stdout.cwl
+++ b/src/_includes/cwl/outputs/stdout.cwl
@@ -7,7 +7,7 @@ stdout: output.txt
 inputs:
   message:
     type: string
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   example_out:

From d589ed66892d1b9a6664163b7e76fa08888ce6b9 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:46:48 +0100
Subject: [PATCH 12/23] change inputBinding field to arguments

---
 src/_includes/cwl/outputs/tar.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/outputs/tar.cwl b/src/_includes/cwl/outputs/tar.cwl
index f1b45964..c0c01c94 100644
--- a/src/_includes/cwl/outputs/tar.cwl
+++ b/src/_includes/cwl/outputs/tar.cwl
@@ -6,7 +6,7 @@ baseCommand: [tar, --extract]
 inputs:
   tarfile:
     type: File
-    inputBinding:
+    arguments:
       prefix: --file
 outputs:
   example_out:

From e58b56daa95bf741ed56af54b7e3ef135cd4815c Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:48:01 +0100
Subject: [PATCH 13/23] Update tar-param.cwl

---
 src/_includes/cwl/parameter-references/tar-param.cwl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/_includes/cwl/parameter-references/tar-param.cwl b/src/_includes/cwl/parameter-references/tar-param.cwl
index 87ad9e0f..51c1d2d4 100644
--- a/src/_includes/cwl/parameter-references/tar-param.cwl
+++ b/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:

From bcb2ab0781a5418f51e7866ac0f4f8f74c09a17e Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:49:58 +0100
Subject: [PATCH 14/23] change inputBinding field to arguments

---
 .../cwl/specifying-software-requirements/custom-types.cwl     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/_includes/cwl/specifying-software-requirements/custom-types.cwl b/src/_includes/cwl/specifying-software-requirements/custom-types.cwl
index 044db0bf..04c71399 100644
--- a/src/_includes/cwl/specifying-software-requirements/custom-types.cwl
+++ b/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
 

From 9db4e4935b0d9d0bb5698d4ec7db243fd227eef9 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:51:07 +0100
Subject: [PATCH 15/23] change inputBinding field to arguments

---
 src/_includes/cwl/staging-input-files/linkfile.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/staging-input-files/linkfile.cwl b/src/_includes/cwl/staging-input-files/linkfile.cwl
index ffeb6996..9a20f8c3 100644
--- a/src/_includes/cwl/staging-input-files/linkfile.cwl
+++ b/src/_includes/cwl/staging-input-files/linkfile.cwl
@@ -15,7 +15,7 @@ requirements:
 inputs:
   src:
     type: File
-    inputBinding:
+    arguments:
       position: 1
       valueFrom: $(self.basename)
 

From 086cd5d69d0c59177081b7a2736249a54cf2e9ec Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:56:26 +0100
Subject: [PATCH 16/23] change inputBinding field to arguments

---
 src/_includes/cwl/using-containers/docker.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/using-containers/docker.cwl b/src/_includes/cwl/using-containers/docker.cwl
index 9f6090a1..43609b7c 100755
--- a/src/_includes/cwl/using-containers/docker.cwl
+++ b/src/_includes/cwl/using-containers/docker.cwl
@@ -9,7 +9,7 @@ hints:
 inputs:
   src:
     type: File
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   example_out:

From 699dc2736d0d89cb4306a3cfa6c41a06cbb68581 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:57:51 +0100
Subject: [PATCH 17/23] change inputBinding field to arguments

---
 src/_includes/cwl/workflows/arguments.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/workflows/arguments.cwl b/src/_includes/cwl/workflows/arguments.cwl
index c26d2642..8d7effdd 100644
--- a/src/_includes/cwl/workflows/arguments.cwl
+++ b/src/_includes/cwl/workflows/arguments.cwl
@@ -11,7 +11,7 @@ arguments: ["-d", $(runtime.outdir)]
 inputs:
   src:
     type: File
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   classfile:

From c8c45f81259e82ee2648a8d642a3b85b5e224ebd Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:58:39 +0100
Subject: [PATCH 18/23] change inputBinding field to arguments

---
 src/_includes/cwl/workflows/hello_world.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/workflows/hello_world.cwl b/src/_includes/cwl/workflows/hello_world.cwl
index 48e2f792..1871a3d9 100755
--- a/src/_includes/cwl/workflows/hello_world.cwl
+++ b/src/_includes/cwl/workflows/hello_world.cwl
@@ -6,7 +6,7 @@ baseCommand: echo
 inputs:
   message:
     type: string
-    inputBinding:
+    arguments:
       position: 1
 outputs:
   echo_out:

From 1ae9c3a54b5f14c7cc5f6b2d0cd436c0440ae02e Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 13:59:13 +0100
Subject: [PATCH 19/23] change inputBinding field to arguments

---
 src/_includes/cwl/workflows/hello_world_to_stdout.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/workflows/hello_world_to_stdout.cwl b/src/_includes/cwl/workflows/hello_world_to_stdout.cwl
index 1d550fc2..2612b433 100755
--- a/src/_includes/cwl/workflows/hello_world_to_stdout.cwl
+++ b/src/_includes/cwl/workflows/hello_world_to_stdout.cwl
@@ -6,6 +6,6 @@ baseCommand: echo
 inputs:
   message:
     type: string
-    inputBinding:
+    arguments:
       position: 1
 outputs: []

From 1ac0f6c4f6d5b664de980388433663993d2f220c Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 14:00:48 +0100
Subject: [PATCH 20/23] change inputBinding field to arguments

---
 src/_includes/cwl/workflows/tar-param.cwl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/_includes/cwl/workflows/tar-param.cwl b/src/_includes/cwl/workflows/tar-param.cwl
index 87ad9e0f..51c1d2d4 100644
--- a/src/_includes/cwl/workflows/tar-param.cwl
+++ b/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:

From b1e28884e50759c2f1b86b444fae3a9d3b144825 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 14:01:34 +0100
Subject: [PATCH 21/23] change inputBinding field to arguments

---
 src/_includes/cwl/workflows/wc-tool.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/workflows/wc-tool.cwl b/src/_includes/cwl/workflows/wc-tool.cwl
index c3064634..480cba12 100755
--- a/src/_includes/cwl/workflows/wc-tool.cwl
+++ b/src/_includes/cwl/workflows/wc-tool.cwl
@@ -7,6 +7,6 @@ arguments: ["-c"]
 inputs:
   input_file:
     type: File
-    inputBinding:
+    arguments:
       position: 1
 outputs: []

From 50574fb1e3dfea128c44a2b0be1b6cff8b44316e Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 14:02:22 +0100
Subject: [PATCH 22/23] change inputBinding field to arguments

---
 src/_includes/cwl/echo.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/echo.cwl b/src/_includes/cwl/echo.cwl
index 6248ae84..e914873f 100644
--- a/src/_includes/cwl/echo.cwl
+++ b/src/_includes/cwl/echo.cwl
@@ -8,7 +8,7 @@ stdout: output.txt
 inputs:
   message:
     type: string
-    inputBinding: {}
+    arguments: {}
 outputs:
   out:
     type: string

From 6fcfd549faf543ec2916e90da13b239b93747a03 Mon Sep 17 00:00:00 2001
From: Ngumih Fien <72187339+Fienne@users.noreply.github.com>
Date: Sun, 23 Oct 2022 14:02:57 +0100
Subject: [PATCH 23/23] change inputBinding field to arguments

---
 src/_includes/cwl/hello_world.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/_includes/cwl/hello_world.cwl b/src/_includes/cwl/hello_world.cwl
index 3d35dbb8..4ac26fcd 100644
--- a/src/_includes/cwl/hello_world.cwl
+++ b/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: []