# HG changeset patch
# User bgruening
# Date 1754902389 0
# Node ID 0811613196a2de8808c8cdfc6bb62cb56c1667a7
# Parent  a88a1e78702efe52f5eb362d3a8bae6bdea3d731
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1180d1e85b63beb3d2e7fd6e9c73b054a9348e7f

diff -r a88a1e78702e -r 0811613196a2 macros.xml
--- a/macros.xml	Sun Jun 22 12:25:48 2025 +0000
+++ b/macros.xml	Mon Aug 11 08:53:09 2025 +0000
@@ -1,10 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">1.3.0</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">23.0</token>
     <xml name="requirements">
         <requirements>
-            <container type="docker">quay.io/bgruening/vpt:1.3.0-1</container>
+            <container type="docker">quay.io/bgruening/vpt:1.3.0-2</container>
             <yield/>
         </requirements>
     </xml>
@@ -17,7 +17,7 @@
         </creator>
     </xml>
     <token name="@CMD@"><![CDATA[
-        mkdir -p 'input/images' 'output/' &&
+        mkdir -p 'input/images' 'input/model' 'output/' &&
         #for $image in $input_images:
             ln -s '$image' 'input/images/${image.element_identifier}.${image.ext}' &&
         #end for
@@ -25,7 +25,6 @@
         ]]></token>
     <token name="@COMMON_ARGS@"><![CDATA[
         --processes \${GALAXY_SLOTS:-10}
-        --verbose
         --log-file 'output/log'
     ]]>
     </token>
diff -r a88a1e78702e -r 0811613196a2 safetensors_convert_pytorch.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/safetensors_convert_pytorch.py	Mon Aug 11 08:53:09 2025 +0000
@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+import sys
+
+import torch
+from safetensors import safe_open
+from safetensors.torch import save_file
+
+
+def convert_pt_to_safetensors(input_path, output_path):
+    """Convert PyTorch model to SafeTensors format."""
+    print(f"Loading PyTorch model from: {input_path}")
+
+    try:
+        # Load the PyTorch model
+        state_dict = torch.load(input_path)
+
+        print(f"Converting {len(state_dict)} tensors to SafeTensors format...")
+
+        # Save as SafeTensors
+        save_file(state_dict, output_path)
+        print(f"Successfully converted to SafeTensors: {output_path}")
+
+    except Exception as e:
+        print(f"Error converting PyTorch to SafeTensors: {e}")
+        sys.exit(1)
+
+
+def convert_safetensors_to_pt(input_path, output_path):
+    """Convert SafeTensors to PyTorch format."""
+    print(f"Loading SafeTensors model from: {input_path}")
+
+    try:
+        state_dict = {}
+
+        # Load SafeTensors
+        with safe_open(input_path, framework="pt", device="cpu") as f:
+            for key in f.keys():
+                state_dict[key] = f.get_tensor(key)
+
+        print(f"Converting {len(state_dict)} tensors to PyTorch format...")
+
+        # Save as PyTorch
+        torch.save(state_dict, output_path)
+        print(f"Successfully converted to PyTorch: {output_path}")
+
+    except Exception as e:
+        print(f"Error converting SafeTensors to PyTorch: {e}")
+        sys.exit(1)
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Convert between PyTorch and SafeTensors",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  python converter.py --convert pt_safe -i model.pt -o model.safetensors
+  python converter.py --convert safe_pt -i model.safetensors -o model.pt
+        """
+    )
+
+    parser.add_argument(
+        "--convert",
+        required=True,
+        choices=["pt_safe", "safe_pt"],
+        help=(
+            "Conversion direction: 'pt_safe' (PyTorch to SafeTensors) "
+            "or 'safe_pt' (SafeTensors to PyTorch)"
+        )
+    )
+
+    parser.add_argument(
+        "-i", "--input",
+        required=True,
+        help="Input model file path"
+    )
+
+    parser.add_argument(
+        "-o", "--output",
+        required=True,
+        help="Output model file path"
+    )
+
+    args = parser.parse_args()
+
+    # Validate input file exists
+    if not os.path.exists(args.input):
+        print(f"Error: Input file does not exist: {args.input}")
+        sys.exit(1)
+
+    # Create output directory if it doesn't exist
+    output_dir = os.path.dirname(args.output)
+    if output_dir and not os.path.exists(output_dir):
+        os.makedirs(output_dir)
+        print(f"Created output directory: {output_dir}")
+
+    # Perform conversion
+    if args.convert == "pt_safe":
+
+        convert_pt_to_safetensors(args.input, args.output)
+
+    elif args.convert == "safe_pt":
+
+        convert_safetensors_to_pt(args.input, args.output)
+
+    print("Conversion completed successfully!")
+
+
+if __name__ == "__main__":
+    main()
diff -r a88a1e78702e -r 0811613196a2 vpt_segment.xml
--- a/vpt_segment.xml	Sun Jun 22 12:25:48 2025 +0000
+++ b/vpt_segment.xml	Mon Aug 11 08:53:09 2025 +0000
@@ -5,10 +5,19 @@
     </macros>
     <expand macro="requirements" />
     <expand macro="creator" />
+    <required_files>
+        <include path="safetensors_convert_pytorch.py"/>
+    </required_files>
     <command detect_errors="exit_code"><![CDATA[
         @CMD@
         ln -s '$detected_transcripts' 'input/detected_transcripts.csv' &&
         ln -s '$vpt_config_file' 'input/vpt_config_file.json' &&
+        #for $i, $task in enumerate($vpt_config.segmentation_tasks.segmentation_task):
+            #if $task.segmentation_properties.custom_weights:
+            ln -s '$task.segmentation_properties.custom_weights' 'input/model/custom_weights_${i}.safetensors' &&
+            python '$__tool_directory__/safetensors_convert_pytorch.py' --convert safe_pt -i 'input/model/custom_weights_${i}.safetensors' -o 'input/model/custom_weights_${i}.pth' &&
+            #end if
+        #end for
         ### segmentation
         vpt
             @COMMON_ARGS@
@@ -105,7 +114,7 @@
             #end if
             "model_dimensions": "$task.segmentation_properties.model_dimensions",
             #if $task.segmentation_properties.custom_weights:
-            "custom_weights": "$task.segmentation_properties.custom_weights",
+            "custom_weights": "input/model/custom_weights_${i}.pth",
             #else:
             "custom_weights": null,
             #end if
@@ -351,7 +360,7 @@
                             <option value="2D">2D</option>
                             <option value="3D">3D</option>
                         </param>
-                        <param argument="--custom_weights" type="data" format="data" optional="true" label="Custom Cellpose weights file"/>
+                        <param argument="--custom_weights" type="data" format="safetensors" optional="true" label="Custom Cellpose weights file"/>
                         <section name="channel_map" title="Channel map" expanded="true" help="Specify the channel map for the segmentation task with the corresponding task input data">
                             <conditional name="channel_red_conditional">
                                 <param name="red" type="select" label="The stain that will be used for red channel">
@@ -553,21 +562,20 @@
                     <assert_contents>
                         <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
                         <has_text_matching expression=",752.854533232[0-9]+,315.600965641[0-9]+,5.50107977386[0-9]+,310.1669732237[0-9]+,"/>
-                        <has_text_matching expression=",416.540438981[0-9]+,68.7110642977[0-9]+,9.67291568732[0-9]+,64.4947481953[0-9]+,"/>
+                        <has_text_matching expression=",777.13824141[0-9]+,70.4487975801[0-9]+,1.976992703078[0-9]+,65.5065863409[0-9]+,"/>
                     </assert_contents>
                 </element>
                 <element name="detected_transcripts">
                     <assert_contents>
                         <has_text_matching expression=",barcode_id,global_x,global_y,global_z,x,y,fov,gene,transcript_id,cell_id"/>
-                        <has_text_matching expression="86,10,285.00012,10.13364,0.0,816.0,153.0,0,AKAP11,ENST00000025301.3"/>
-                        <has_text_matching expression="229,10,274.95612,35.72964,0.0,723.0,390.0,0,AKAP11,ENST00000025301.3"/>
+                        <has_text_matching expression="63,10,370.95007,5.520504,0.0,1611.833,110.285774,0,AKAP11,ENST00000025301.3"/>
+                        <has_text_matching expression="68,10,355.46716,6.4616404,0.0,1468.4725,119.0,0,AKAP11,ENST00000025301.3"/>
                     </assert_contents>
                 </element>
                 <element name="metrics">
                     <assert_contents>
                         <has_text_matching expression=",Cell count,Cell volume"/>
-                        <has_text_matching expression="All cells,814,1572.4,1533.3,735.8,654.0,92.1,108.0,96.4,68.2,0.0"/>
-                        <has_text_matching expression="Cells after filtering,700,1694.1,1667.9,851.1,810.5,104.5,111.0,95.9,63.2,0.06"/>
+                        <has_n_lines n="3"/>
                     </assert_contents>
                 </element>
                 <element name="sum_signals">
@@ -762,8 +770,7 @@
                 <element name="metrics">
                     <assert_contents>
                         <has_text_matching expression=",Cell count,Cell volume"/>
-                        <has_text_matching expression="All cells,811,1588.0,1549.9,740.5,669.0,92.2,109.0,96.7,68.6,0.0"/>
-                        <has_text_matching expression="Cells after filtering,698,1711.6,1705.9,856.1,817.5,104.6,111.0,96.2,63.7,0.06"/>
+                        <has_n_lines n="3"/>
                     </assert_contents>
                 </element>
                 <element name="sum_signals">
@@ -834,7 +841,7 @@
                         <section name="segmentation_properties">
                             <param name="model" value="null"/>
                             <param name="model_dimensions" value="2D"/>
-                            <param name="custom_weights" location="https://zenodo.org/records/15319018/files/CP_20230830_093420"/>
+                            <param name="custom_weights" location="https://zenodo.org/records/16784480/files/CP_20230830_093420.safetensors"/>
                             <section name="channel_map">
                                 <conditional name="channel_red_conditional">
                                     <param name="red" value="Cellbound1"/>
@@ -905,14 +912,14 @@
                 <element name="cell_by_gene">
                     <assert_contents>
                         <has_text_matching expression="cell,AKAP11,CBX5,CCDC113"/>
-                        <has_text_matching expression="6,11,4,0,5,2,1,0,1,2,1,2"/>
-                        <has_text_matching expression="0,1,0,0,0,0,1,0,0,4"/>
+                        <has_text_matching expression="6,10,4,0,5,2,1,0,1,2"/>
+                        <has_text_matching expression="0,1,0,0,0,0,1,0,0,4,0"/>
                     </assert_contents>
                 </element>
                 <element name="cell_metadata">
                     <assert_contents>
                         <has_text_matching expression="EntityID,fov,volume,center_x,center_y,min_x,min_y,max_x,max_y,anisotropy,transcript_count,perimeter_area_ratio,solidity"/>
-                        <has_text_matching expression="168.0683921161[0-9]+,246.3592447472[0-9]+,-1.507707574380[0-9]+,243.9322371166[0-9]+"/>
+                        <has_text_matching expression="167.0695914980[0-9]+,246.371389688[0-9]+,-1.502969079760[0-9]+,243.9322371166[0-9]+"/>
                         <has_text_matching expression="1540.721726928[0-9]+,412.175889439[0-9]+,2.951632912099[0-9]+,404.3500198495[0-9]+"/>
                     </assert_contents>
                 </element>
@@ -926,14 +933,13 @@
                 <element name="metrics">
                     <assert_contents>
                         <has_text_matching expression=",Cell count,Cell volume"/>
-                        <has_text_matching expression="All cells,93[0-9]+,121\d*(\.\d+)?,118\d*(\.\d+)?,60\d*(\.\d+)?,49\d*(\.\d+)?,7\d*(\.\d+)?,10\d*(\.\d+)?,9\d*(\.\d+)?,6\d*(\.\d+)?,0.0"/>
-                        <has_text_matching expression="Cells after filtering,659,1532.9,1553.5,850.2,837.0,104.8,112.0,90.2,53.8,0.15"/>
+                        <has_n_lines n="3"/>
                     </assert_contents>
                 </element>
                 <element name="sum_signals">
                     <assert_contents>
                         <has_text_matching expression="Cellbound2_raw,Cellbound2_high_pass"/>
-                        <has_text_matching expression="73446567.0,1605103.666715[0-9]+"/>
+                        <has_text_matching expression="72859278.0,1502895.008866[0-9]+"/>
                         <has_text_matching expression="1642190888.0,16154095.44810[0-9]+"/>
                     </assert_contents>
                 </element>
@@ -972,6 +978,7 @@
                         <has_text_matching expression="null"/>
                         <has_text_matching expression="CLAHE"/>
                         <has_text_matching expression="harmonize"/>
+                        <has_text_matching expression="input/model/custom_weights_0.pth"/>
                     </assert_contents>
                 </element>
             </output_collection>