changed repository name to make it valid

tools/zeiss_lmd_converter/.shed.yml

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+categories:
+  - Proteomics
+description: Converts coordinates from a tabular file into a formatted text file readable by Zeiss laser-capture microdissection systems
+long_description: |
+   This tool is part of a workflow that allows to use tissue anontations in geojson format from machine learning based imaging software like QuPath and HaloAI and transform these annotation coordinates into a text format readable by Zeiss laser-capture microdissection systems
+owner: galaxyp
+remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter
+homepage_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter
+type: unrestricted

tools/zeiss_lmd_converter/tabular_to_ZeissLMDtext.py

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+import argparse
+from shapely.geometry import Polygon
+
+def tabular_to_text(input_file, text_file):
+    """
+    Converts tabular coordinate data from Galaxy into a formatted text file which is readable for the LMD.
+
+    This function reads tabular data from an input file, processes it to form a closed polygon, calculates the area
+    of the polygon, and writes the formatted information to an output text file.
+
+    Parameters:
+    input_file (str): Path to the input file containing tabular coordinate data.
+                      The file should have a header and each line should contain x and y coordinates separated by a tab.
+    text_file (str): Path to the output text file where the formatted information will be written.
+
+    The output text file will contain:
+    - Header information
+    - A section with metadata including version, date, and time
+    - A section with details of the polygon including type, color, thickness, number, cutshot, area, comment,
+      and coordinates.
+    """
+    coordinates = []
+    with open(input_file, 'r') as f:
+        next(f)  # Skip the header
+        for line in f:
+            x, y = map(float, line.strip().split('\t'))
+            coordinates.append([x, y])
+
+    coordinates.append(coordinates[0])  # Close the polygon by repeating the first point as the last point
+    area = Polygon(coordinates).area
+
+    with open(text_file, 'w') as f:
+        f.write("PALMRobo Elements\n")
+        f.write("Version:\tV 4.6.0.4\n")
+        f.write("Date, Time:\t13.02.2024\t16:06:32\n")
+        f.write("\nMICROMETER\nElements :\n\nType\tColor\tThickness\tNo\tCutShot\tArea\tComment\tCoordinates\n\n")
+        f.write(f"Freehand\tgreen\t0\t7\t0,0\t{area}\tROI imported from tabular data\n")
+
+        for i in range(0, len(coordinates), 5):
+            for j in range(5):
+                if i + j < len(coordinates):
+                    x, y = coordinates[i + j]
+                    f.write(f"\t{x},{y}")
+            f.write("\n.")
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description="Convert tabular coordinate data into a formatted text file")
+    parser.add_argument('--input', type=str, required=True, help='Path to the input tabular file')
+    parser.add_argument('--output', type=str, required=True, help='Path to the output text file')
+    args = parser.parse_args()
+
+    tabular_to_text(args.input, args.output)
+

tools/zeiss_lmd_converter/test-data/Zeiss_converted_file_small.txt

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+PALMRobo Elements
+Version:	V 4.6.0.4
+Date, Time:	13.02.2024	16:06:32
+
+MICROMETER
+Elements :
+
+Type	Color	Thickness	No	CutShot	Area	Comment	Coordinates
+
+Freehand	green	0	7	0,0	23955.0	ROI imported from tabular data
+	1.0,1.0	200.0,200.0	300.0,100.0	200.0,50.0	100.0,10.0
+.	1.0,1.0
+.