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(-) [+]
line wrap: on
line diff
--- /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
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+.	70850.2,31047.7	70811.7,31281.3
+.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Zeiss_converted_file_small.txt	Mon Jul 01 14:07:46 2024 +0000
@@ -0,0 +1,13 @@
+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
+.
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coordinates_x_y.tabular	Mon Jul 01 14:07:46 2024 +0000
@@ -0,0 +1,1667 @@
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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>