From 74a7374ad669236834542b9815350c87b129cf32 Mon Sep 17 00:00:00 2001
From: SooLee <duplexa@gmail.com>
Date: Tue, 5 Dec 2017 12:22:01 -0500
Subject: [PATCH] added make_referencebg

---
 cwl_awsem/repliseq/make_referencebg.cwl | 72 +++++++++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 cwl_awsem/repliseq/make_referencebg.cwl

diff --git a/cwl_awsem/repliseq/make_referencebg.cwl b/cwl_awsem/repliseq/make_referencebg.cwl
new file mode 100644
index 0000000..d818c0b
--- /dev/null
+++ b/cwl_awsem/repliseq/make_referencebg.cwl
@@ -0,0 +1,72 @@
+{
+    "outputs": [
+        {
+            "id": "#out_reference_bg",
+            "type": [
+                "null",
+                "File"
+            ],
+            "outputBinding": {
+                "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.inorm.bg')"
+            }
+        }
+    ],
+    "baseCommand": [
+        "make_referencebg"
+    ],
+    "hints": [
+        {
+            "dockerPull": "duplexa/4dn-repliseq:v9",
+            "class": "DockerRequirement"
+        }
+    ],
+    "cwlVersion": "draft-3",
+    "class": "CommandLineTool",
+    "arguments": [],
+    "inputs": [
+        {
+            "id": "#outdir",
+            "inputBinding": {
+                "position": 1,
+                "separate": true
+            },
+            "default": ".",
+            "type": [
+                "null",
+                "string"
+            ]
+        },
+        {
+            "id": "#outprefix",
+            "inputBinding": {
+                "position": 2,
+                "separate": true
+            },
+            "default": "out",
+            "type": [
+                "null",
+                "string"
+            ]
+        },
+        {
+            "id": "#input_bgs",
+            "inputBinding": {
+                "itemSeparator": " ",
+                "position": 3,
+                "separate": true
+            },
+            "type": [
+                "null",
+                {
+                    "items": "File",
+                    "type": "array"
+                }
+            ]
+        }
+    ],
+    "requirements": [
+        {
+            "class": "InlineJavascriptRequirement"
+        }
+    ]
+}