From 06ee052692eb824c14d042083ba02d7287523d34 Mon Sep 17 00:00:00 2001
From: Rob Marissen <50015273+524D@users.noreply.github.com>
Date: Wed, 16 Oct 2024 09:13:31 +0200
Subject: [PATCH] Add Wordcloud (#76)

Added wcloud
---
 cwl-tools/wcloud/tool.json                 | 17 +++++++++++++
 cwl-tools/wcloud/wcloud.cwl                | 29 ++++++++++++++++++++++
 domains/proteomics/included_bio.tools.json |  3 ++-
 domains/proteomics/tools.json              | 17 +++++++++++++
 4 files changed, 65 insertions(+), 1 deletion(-)
 create mode 100644 cwl-tools/wcloud/tool.json
 create mode 100644 cwl-tools/wcloud/wcloud.cwl

diff --git a/cwl-tools/wcloud/tool.json b/cwl-tools/wcloud/tool.json
new file mode 100644
index 0000000..469f232
--- /dev/null
+++ b/cwl-tools/wcloud/tool.json
@@ -0,0 +1,17 @@
+[{
+    "outputs": [{
+        "format_1915": ["http://edamontology.org/format_3603"],
+        "data_0006": ["http://edamontology.org/data_2968"]
+    }],
+    "biotoolsID": "wcloud",
+    "inputs": [{
+        "format_1915": ["http://edamontology.org/format_2330"],
+        "data_0006": ["http://edamontology.org/data_2526"]
+    }],
+    "implementation": {
+        "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/wcloud/wcloud.cwl"
+    },
+    "taxonomyOperations": ["http://edamontology.org/operation_0337"],
+    "label": "wcloud",
+    "id": "wcloud"
+}]
\ No newline at end of file
diff --git a/cwl-tools/wcloud/wcloud.cwl b/cwl-tools/wcloud/wcloud.cwl
new file mode 100644
index 0000000..6112229
--- /dev/null
+++ b/cwl-tools/wcloud/wcloud.cwl
@@ -0,0 +1,29 @@
+# The template for this tool description is generated by APE (https://github.com/sanctuuary/APE).
+cwlVersion: v1.2
+class: CommandLineTool
+baseCommand: wcloud
+label: wcloud
+requirements:
+  ShellCommandRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.wcloud_in_0)
+  DockerRequirement:
+    dockerPull: robmarissen/wcloud:21aee44
+arguments: ["--output", "output.png", "--background-color", "white", "--width", "1200", "--height", "800"]
+
+inputs:
+  wcloud_in_0:
+    type: File
+    format: "http://edamontology.org/format_2330" # Textual format
+    inputBinding:
+      prefix: --text
+      valueFrom: $(self.basename)
+
+outputs:
+  wcloud_out_0:
+    type: File
+    format: "http://edamontology.org/format_3603" # PNG
+    outputBinding:
+      glob: "output.png"
+
diff --git a/domains/proteomics/included_bio.tools.json b/domains/proteomics/included_bio.tools.json
index 7264470..5441a75 100644
--- a/domains/proteomics/included_bio.tools.json
+++ b/domains/proteomics/included_bio.tools.json
@@ -11,5 +11,6 @@
     "XTandem",
     "ms_amanda",
     "msfragger",
-    "protXml2IdList"
+    "protXml2IdList",
+    "wcloud"
 ]
diff --git a/domains/proteomics/tools.json b/domains/proteomics/tools.json
index a7a8fff..bec809e 100644
--- a/domains/proteomics/tools.json
+++ b/domains/proteomics/tools.json
@@ -454,6 +454,23 @@
       },
       "label": "Sage",
       "id": "Sage-proteomics"
+    },
+    {
+      "outputs": [{
+          "format_1915": ["http://edamontology.org/format_3603"],
+          "data_0006": ["http://edamontology.org/data_2968"]
+      }],
+      "biotoolsID": "wcloud",
+      "inputs": [{
+          "format_1915": ["http://edamontology.org/format_2330"],
+          "data_0006": ["http://edamontology.org/data_2526"]
+      }],
+      "implementation": {
+          "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/wcloud/wcloud.cwl"
+      },
+      "taxonomyOperations": ["http://edamontology.org/operation_0337"],
+      "label": "wcloud",
+      "id": "wcloud"
     }
   ]
 }