Convert output types from File to String

childmindresearch · Dec 18, 2024 · a6b96c7 · a6b96c7
1 parent 83a5959
commit a6b96c7
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Showing 2 changed files with 56 additions and 27 deletions.
diff --git a/descriptors/fsl/fugue.json b/descriptors/fsl/fugue.json
@@ -67,7 +67,7 @@
     {
       "id": "fmap_out_file",
       "name": "Fmap out file",
-      "type": "File",
+      "type": "String",
       "value-key": "[FMAP_OUT_FILE]",
       "command-line-flag": "--savefmap",
       "command-line-flag-separator": "=",
@@ -103,7 +103,9 @@
       "command-line-flag": "--icorr",
       "description": "Apply intensity correction to unwarping (pixel shift method only).",
       "optional": true,
-      "requires-inputs": ["shift_in_file"]
+      "requires-inputs": [
+        "shift_in_file"
+      ]
     },
     {
       "id": "icorr_only",
@@ -113,7 +115,9 @@
       "command-line-flag": "--icorronly",
       "description": "Apply intensity correction only.",
       "optional": true,
-      "requires-inputs": ["unwarped_file"]
+      "requires-inputs": [
+        "unwarped_file"
+      ]
     },
     {
       "id": "in_file",
@@ -178,7 +182,12 @@
       "value-key": "[OUTPUT_TYPE]",
       "description": "'nifti' or 'nifti_pair' or 'nifti_gz' or 'nifti_pair_gz'. Fsl output type.",
       "optional": true,
-      "value-choices": ["NIFTI", "NIFTI_PAIR", "NIFTI_GZ", "NIFTI_PAIR_GZ"]
+      "value-choices": [
+        "NIFTI",
+        "NIFTI_PAIR",
+        "NIFTI_GZ",
+        "NIFTI_PAIR_GZ"
+      ]
     },
     {
       "id": "pava",
@@ -268,7 +277,7 @@
     {
       "id": "shift_out_file",
       "name": "Shift out file",
-      "type": "File",
+      "type": "String",
       "value-key": "[SHIFT_OUT_FILE]",
       "command-line-flag": "--saveshift",
       "command-line-flag-separator": "=",
@@ -304,29 +313,40 @@
       "command-line-flag-separator": "=",
       "description": "'x' or 'y' or 'z' or 'x-' or 'y-' or 'z-'. Specifies direction of warping (default y).",
       "optional": true,
-      "value-choices": ["x", "y", "z", "x-", "y-", "z-"]
+      "value-choices": [
+        "x",
+        "y",
+        "z",
+        "x-",
+        "y-",
+        "z-"
+      ]
     },
     {
       "id": "unwarped_file",
       "name": "Unwarped file",
-      "type": "File",
+      "type": "String",
       "value-key": "[UNWARPED_FILE]",
       "command-line-flag": "--unwarp",
       "command-line-flag-separator": "=",
       "description": "Apply unwarping and save as filename.",
       "optional": true,
-      "requires-inputs": ["in_file"]
+      "requires-inputs": [
+        "in_file"
+      ]
     },
     {
       "id": "warped_file",
       "name": "Warped file",
-      "type": "File",
+      "type": "String",
       "value-key": "[WARPED_FILE]",
       "command-line-flag": "--warp",
       "command-line-flag-separator": "=",
       "description": "Apply forward warping and save as filename.",
       "optional": true,
-      "requires-inputs": ["in_file"]
+      "requires-inputs": [
+        "in_file"
+      ]
     }
   ],
   "output-files": [
@@ -363,19 +383,28 @@
     {
       "id": "mutex_group",
       "name": "Mutex group",
-      "members": ["warped_file", "unwarped_file"],
+      "members": [
+        "warped_file",
+        "unwarped_file"
+      ],
       "mutually-exclusive": true
     },
     {
       "id": "mutex_group_2",
       "name": "Mutex group 2",
-      "members": ["save_unmasked_shift", "save_shift"],
+      "members": [
+        "save_unmasked_shift",
+        "save_shift"
+      ],
       "mutually-exclusive": true
     },
     {
       "id": "mutex_group_3",
       "name": "Mutex group 3",
-      "members": ["save_fmap", "save_unmasked_fmap"],
+      "members": [
+        "save_fmap",
+        "save_unmasked_fmap"
+      ],
       "mutually-exclusive": true
     }
   ],
@@ -385,4 +414,4 @@
     "type": "docker",
     "image": "brainlife/fsl:6.0.4-patched2"
   }
-}
+}
diff --git a/python/src/niwrap/fsl/fugue.py b/python/src/niwrap/fsl/fugue.py
@@ -7,7 +7,7 @@
 import dataclasses
 
 FUGUE_METADATA = Metadata(
-    id="d264261226a39feda65ebd1686c5c1c1076e293f.boutiques",
+    id="e92886e40bebff1fca6ad036e63b3a6f487c4e4c.boutiques",
     name="fugue",
     package="fsl",
     container_image_tag="brainlife/fsl:6.0.4-patched2",
@@ -37,7 +37,7 @@ def fugue(
     dwell_time: float | None = None,
     dwell_to_asym_ratio: float | None = None,
     fmap_in_file: InputPathType | None = None,
-    fmap_out_file: InputPathType | None = None,
+    fmap_out_file: str | None = None,
     forward_warping: bool = False,
     fourier_order: int | None = None,
     icorr: bool = False,
@@ -58,12 +58,12 @@ def fugue(
     save_unmasked_fmap: bool = False,
     save_unmasked_shift: bool = False,
     shift_in_file: InputPathType | None = None,
-    shift_out_file: InputPathType | None = None,
+    shift_out_file: str | None = None,
     smooth2d: float | None = None,
     smooth3d: float | None = None,
     unwarp_direction: typing.Literal["x", "y", "z", "x-", "y-", "z-"] | None = None,
-    unwarped_file: InputPathType | None = None,
-    warped_file: InputPathType | None = None,
+    unwarped_file: str | None = None,
+    warped_file: str | None = None,
     runner: Runner | None = None,
 ) -> FugueOutputs:
     """
@@ -133,7 +133,7 @@ def fugue(
     if fmap_in_file is not None:
         cargs.append("--loadfmap=" + execution.input_file(fmap_in_file))
     if fmap_out_file is not None:
-        cargs.append("--savefmap=" + execution.input_file(fmap_out_file))
+        cargs.append("--savefmap=" + fmap_out_file)
     if forward_warping:
         cargs.append("--forward_warping")
     if fourier_order is not None:
@@ -175,23 +175,23 @@ def fugue(
     if shift_in_file is not None:
         cargs.append("--loadshift=" + execution.input_file(shift_in_file))
     if shift_out_file is not None:
-        cargs.append("--saveshift=" + execution.input_file(shift_out_file))
+        cargs.append("--saveshift=" + shift_out_file)
     if smooth2d is not None:
         cargs.append("--smooth2=" + str(smooth2d))
     if smooth3d is not None:
         cargs.append("--smooth3=" + str(smooth3d))
     if unwarp_direction is not None:
         cargs.append("--unwarpdir=" + unwarp_direction)
     if unwarped_file is not None:
-        cargs.append("--unwarp=" + execution.input_file(unwarped_file))
+        cargs.append("--unwarp=" + unwarped_file)
     if warped_file is not None:
-        cargs.append("--warp=" + execution.input_file(warped_file))
+        cargs.append("--warp=" + warped_file)
     ret = FugueOutputs(
         root=execution.output_file("."),
-        fmap_out_file_outfile=execution.output_file(pathlib.Path(fmap_out_file).name) if (fmap_out_file is not None) else None,
-        shift_out_file_outfile=execution.output_file(pathlib.Path(shift_out_file).name) if (shift_out_file is not None) else None,
-        unwarped_file_outfile=execution.output_file(pathlib.Path(unwarped_file).name) if (unwarped_file is not None) else None,
-        warped_file_outfile=execution.output_file(pathlib.Path(warped_file).name) if (warped_file is not None) else None,
+        fmap_out_file_outfile=execution.output_file(fmap_out_file) if (fmap_out_file is not None) else None,
+        shift_out_file_outfile=execution.output_file(shift_out_file) if (shift_out_file is not None) else None,
+        unwarped_file_outfile=execution.output_file(unwarped_file) if (unwarped_file is not None) else None,
+        warped_file_outfile=execution.output_file(warped_file) if (warped_file is not None) else None,
     )
     execution.run(cargs)
     return ret