Update tool paths to biotoolsID and introduce a tool annotation - tool.json file for each tool

cwl-tools/Sage-proteomics/tool.json

@@ -0,0 +1,28 @@
+[
+  {
+    "outputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_3247"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+      }
+    ],
+    "biotoolsID": "Sage-proteomics",
+    "inputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_3244"],
+        "data_0006": ["http://edamontology.org/data_0943"]
+      },
+      {
+        "format_1915": ["http://edamontology.org/format_1929"],
+        "data_0006": ["http://edamontology.org/data_2976"]
+      }
+    ],
+    "taxonomyOperations": [
+      "http://edamontology.org/operation_3631",
+      "http://edamontology.org/operation_3633",
+      "http://edamontology.org/operation_2428"
+    ],
+    "label": "Sage",
+    "id": "Sage-proteomics"
+  }
+]

cwl-tools/Comet/Comet.cwl → cwl-tools/comet/comet.cwl

@@ -1,4 +1,4 @@
-cwlVersion: v1.0
+cwlVersion: v1.2
 class: CommandLineTool
 baseCommand: comet
 label: comet-ms
@@ -21,7 +21,7 @@ inputs:
       separate: false
     default:
       class: File
-      location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/Comet/comet.params
+      location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/comet/comet.params
   Comet_in_1:
     type: File
     format: "http://edamontology.org/format_3244" # mzML

cwl-tools/comet/tool.json

@@ -0,0 +1,38 @@
+[{
+    "outputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_3655"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+      },
+      {
+        "format_1915": ["http://edamontology.org/format_3247"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+      },
+      {
+        "format_1915": ["http://edamontology.org/format_3475"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+      }
+    ],
+    "inputs": [
+      {
+        "format_1915": [
+          "http://edamontology.org/format_3244",
+          "http://edamontology.org/format_3654",
+          "http://edamontology.org/format_3651"
+        ],
+        "data_0006": ["http://edamontology.org/data_0943"]
+      },
+      {
+        "format_1915": ["http://edamontology.org/format_1929"],
+        "data_0006": ["http://edamontology.org/data_2976"]
+      }
+    ],
+    "taxonomyOperations": ["http://edamontology.org/operation_3646"],
+
+    "implementation": {
+      "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/comet/comet.cwl"
+    },
+    "biotoolsID": "comet",
+    "label": "Comet",
+    "id": "Comet"
+  }]

cwl-tools/goenrichment/tool.json

@@ -0,0 +1,36 @@
+{
+    "outputs": [
+      {
+        "format_1915": [
+          "http://edamontology.org/format_3603",
+          "http://edamontology.org/format_2330"
+        ],
+        "data_0006": ["http://edamontology.org/data_3754"]
+      }
+    ],
+    "inputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_2330"],
+        "data_0006": ["http://edamontology.org/data_2872"]
+      },
+      {
+        "format_1915": [
+          "http://edamontology.org/format_2196",
+          "http://edamontology.org/format_2197"
+        ],
+        "data_0006": ["http://edamontology.org/data_0582"]
+      },
+      {
+        "format_1915": ["http://edamontology.org/format_3475"],
+        "data_0006": ["http://edamontology.org/data_0916"]
+      }
+    ],
+    "taxonomyOperations": ["http://edamontology.org/operation_2436"],
+
+    "implementation": {
+      "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/goenrichment/goenrichment.cwl"
+    },
+    "biotoolsID": "goenrichment",
+    "label": "GOEnrichment",
+    "id": "GOEnrichment"
+  }

cwl-tools/gProfiler/gProfiler.cwl → cwl-tools/gprofiler/gprofiler.cwl

@@ -1,6 +1,7 @@
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: ["bash"]
+label: gprofiler
 requirements:
   ShellCommandRequirement: {}
   InitialWorkDirRequirement:
@@ -15,7 +16,7 @@ inputs:
       position: 1
     default:
       class: File
-      location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/gProfiler/gProfiler.sh
+      location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/gprofiler/gprofiler.sh
   gProfiler_in_1:
     type: File
     doc: "Input file containing gene/query data"

cwl-tools/gprofiler/tool.json

@@ -0,0 +1,31 @@
+{
+    "outputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_3464"],
+        "data_0006": [
+          "http://edamontology.org/data_3753",
+          "http://edamontology.org/data_3754",
+          "http://edamontology.org/data_3953"
+        ]
+      }
+    ],
+    "inputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_2330"],
+        "data_0006": ["http://edamontology.org/data_2872"]
+      }
+    ],
+    "taxonomyOperations": [
+      "http://edamontology.org/operation_2422",
+      "http://edamontology.org/operation_3501",
+      "http://edamontology.org/operation_2497",
+      "http://edamontology.org/operation_3672"
+    ],
+
+    "implementation": {
+      "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/gprofiler/gprofiler.cwl"
+    },
+    "biotoolsID": "gprofiler",
+    "label": "gProfiler",
+    "id": "gProfiler"
+  }

cwl-tools/idconvert/idconvert_to_mzIdentML.cwl

@@ -2,7 +2,7 @@
 
 cwlVersion: v1.0
 class: CommandLineTool
-label: idconvert.cwl
+label: idconvert
 
 baseCommand: "/usr/local/tpp/bin/idconvert"
 requirements:

cwl-tools/idconvert/idconvert_to_pepXML.cwl

@@ -2,7 +2,7 @@
 
 cwlVersion: v1.0
 class: CommandLineTool
-label: idconvert.cwl
+label: idconvert
 
 baseCommand: "/usr/local/tpp/bin/idconvert"
 arguments:

cwl-tools/idconvert/tool.json

@@ -0,0 +1,53 @@
+[{
+    "outputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_3655"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+      }
+    ],
+    "inputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_3247"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+      }
+    ],
+    "taxonomyOperations": [
+      "http://edamontology.org/operation_0335",
+      "http://edamontology.org/operation_1812",
+      "http://edamontology.org/operation_3434"
+    ],
+
+    "implementation": {
+      "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/idconvert/idconvert_to_pepXML.cwl"
+    },
+    "biotoolsID": "idconvert",
+    "label": "idconvert",
+    "id": "idconvert_to_pepXML"
+  },
+  {
+    "outputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_3247"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+      }
+    ],
+    "inputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_3655"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+      }
+    ],
+    "taxonomyOperations": [
+      "http://edamontology.org/operation_0335",
+      "http://edamontology.org/operation_1812",
+      "http://edamontology.org/operation_3434"
+    ],
+
+    "implementation": {
+      "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/idconvert/idconvert_to_mzIdentML.cwl"
+    },
+    "biotoolsID": "idconvert",
+    "label": "idconvert",
+    "id": "idconvert_to_mzIdentML"
+  }
+]

cwl-tools/ms_amanda/tool.json

@@ -0,0 +1,35 @@
+{
+    "outputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_3247"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+      }
+    ],
+    "inputs": [
+      {
+        "format_1915": [
+          "http://edamontology.org/format_3244",
+          "http://edamontology.org/format_3651"
+        ],
+        "data_0006": ["http://edamontology.org/data_0943"]
+      },
+      {
+        "format_1915": ["http://edamontology.org/format_1929"],
+        "data_0006": ["http://edamontology.org/data_2976"]
+      }
+    ],
+    "taxonomyOperations": [
+      "http://edamontology.org/operation_2945",
+      "http://edamontology.org/operation_2945",
+      "http://edamontology.org/operation_3767",
+      "http://edamontology.org/operation_3645",
+      "http://edamontology.org/operation_3755"
+    ],
+
+    "implementation": {
+      "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/ms_amanda/ms_amanda.cwl"
+    },
+    "biotoolsID": "ms_amanda",
+    "label": "MS_Amanda",
+    "id": "MS_Amanda"
+  }

cwl-tools/MSFragger/MSFragger.cwl → cwl-tools/msfragger/msfragger.cwl

@@ -22,7 +22,7 @@ inputs:
     type: File
     default:
       class: File
-      location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/MSFragger/fragger.params
+      location: https://raw.githubusercontent.com/Workflomics/tools-and-domains/main/cwl-tools/msfragger/fragger.params
   MSFragger_in_1:
     type: File
     format: "http://edamontology.org/format_3244" # mzML

cwl-tools/msfragger/tool.json

@@ -0,0 +1,33 @@
+{
+    "outputs": [
+      {
+        "format_1915": ["http://edamontology.org/format_3655"],
+        "data_0006": ["http://edamontology.org/data_0945"]
+      }
+    ],
+    "inputs": [
+      {
+        "format_1915": [
+          "http://edamontology.org/format_3244",
+          "http://edamontology.org/format_3654",
+          "http://edamontology.org/format_3651"
+        ],
+        "data_0006": ["http://edamontology.org/data_0943"]
+      },
+      {
+        "format_1915": ["http://edamontology.org/format_1929"],
+        "data_0006": ["http://edamontology.org/data_2976"]
+      }
+    ],
+    "taxonomyOperations": [
+      "http://edamontology.org/operation_2421",
+      "http://edamontology.org/operation_3801"
+    ],
+
+    "implementation": {
+      "cwl_reference": "https://raw.githubusercontent.com/Workflomics/tools-and-domains/refs/heads/main/cwl-tools/msfragger/msfragger.cwl"
+    },
+    "biotoolsID": "msfragger",
+    "label": "MSFragger",
+    "id": "MSFragger"
+  }

cwl-tools/mzRecal/mzRecal.cwl → cwl-tools/mzrecal/mzrecal.cwl

@@ -2,7 +2,7 @@
 
 cwlVersion: v1.0
 class: CommandLineTool
-label: mzRecal.cwl
+label: mzrecal
 requirements:
   DockerRequirement:
     dockerPull: workflomics/mzrecal:1.1.3