Mercurial > repos > galaxyp > zeiss_lmd_converter
changeset 0:f17bc16fefcf draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/zeiss_lmd_converter commit 17fc7ee7911e0b875aaed5be4a129cfea208c76f
| author | galaxyp |
|---|---|
| date | Mon, 01 Jul 2024 14:07:46 +0000 |
| parents | |
| children | |
| files | tabular_to_ZeissLMDtext.py test-data/Zeiss_converted_file.txt test-data/Zeiss_converted_file_small.txt test-data/coordinates_x_y.tabular test-data/coordinates_x_y_small.tabular zeiss_lmd_converter.xml |
| diffstat | 6 files changed, 2120 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tabular_to_ZeissLMDtext.py Mon Jul 01 14:07:46 2024 +0000 @@ -0,0 +1,55 @@ +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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Zeiss_converted_file.txt Mon Jul 01 14:07:46 2024 +0000 @@ -0,0 +1,345 @@ +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 5331.660000000684 ROI imported from tabular data + 70811.7,31281.3 70811.2,31281.3 70810.8,31281.3 70810.3,31281.3 70809.8,31281.3 +. 70809.4,31281.3 70808.9,31281.3 70808.4,31281.3 70808.0,31281.3 70811.7,31280.8 +. 70807.5,31280.8 70811.7,31280.3 70807.1,31280.3 70811.7,31279.9 70807.1,31279.9 +. 70812.2,31279.4 70807.1,31279.4 70813.1,31278.9 70812.6,31278.9 70807.1,31278.9 +. 70813.6,31278.5 70807.1,31278.5 70813.6,31278.0 70807.1,31278.0 70813.6,31277.6 +. 70807.1,31277.5 70813.6,31277.1 70807.1,31277.1 70813.6,31276.6 70807.1,31276.6 +. 70813.6,31276.2 70807.1,31276.2 70814.0,31275.7 70807.1,31275.7 70815.0,31275.2 +. 70814.5,31275.2 70807.1,31275.2 70815.4,31274.8 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/coordinates_x_y_small.tabular Mon Jul 01 14:07:46 2024 +0000 @@ -0,0 +1,6 @@ +x y +1 1 +200 200 +300 100 +200 50 +100 10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/zeiss_lmd_converter.xml Mon Jul 01 14:07:46 2024 +0000 @@ -0,0 +1,34 @@ +<tool id="ZeissLMDconverter" name="Zeiss laser-capture microdissection converter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> + <description>Converts tabular coordinates into a formatted text file readable by Zeiss laser-capture microdissection systems.</description> + <macros> + <token name="@TOOL_VERSION@">2.0.4</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">shapely</requirement> + </requirements> + <command>python3 '$__tool_directory__/tabular_to_ZeissLMDtext.py' --input '$input' --output '$output'</command> + <inputs> + <param name="input" type="data" format="tabular" label="Tabular file with coordinates" help="The file must have two columns, first with x and second with y coordinates" /> + </inputs> + <outputs> + <data name="output" format="txt" label="${tool.name} on ${on_string}"/> + </outputs> + <tests> + <test> + <param name="input" value="coordinates_x_y.tabular" ftype="tabular"/> + <output name="output" file="Zeiss_converted_file.txt"/> + </test> + <test> + <param name="input" value="coordinates_x_y_small.tabular" ftype="tabular"/> + <output name="output" file="Zeiss_converted_file_small.txt"/> + </test> + </tests> + <help> + This tool reads tabular data containing x and y coordinates, processes it to form a closed polygon, + calculates the polygon's area, and writes a formatted text file readable by the PALM RoboSoftware of Zeiss laser-capture microdissection systems. + </help> + <citations> + <citation type="doi">10.5281/zenodo.5597138</citation> + </citations> +</tool>