changeset 4:99433164b593 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/detection_viz/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf

--- a/detection_viz.py	Wed Dec 18 05:02:11 2019 -0500
+++ b/detection_viz.py	Mon Nov 13 22:11:04 2023 +0000
@@ -1,13 +1,13 @@
 import argparse
-import sys
-import os
 import csv
- 
+
 import matplotlib
+import matplotlib.pyplot as plt
+import skimage.io
+
+
 matplotlib.use('Agg')
-import matplotlib.pyplot as plt
 
-import skimage.io
 
 def plot_circles(file_name, ax, color, stroke_size, radius):
     resfile = open(file_name, 'rb')
@@ -17,11 +17,12 @@
         ax.add_patch(circ)
     resfile.close()
 
+
 def detection_viz(input_file, output_file, tp=None, fn=None, fp=None, stroke_size=3, circle_radius=50):
     img = skimage.io.imread(input_file)
 
     fig = plt.figure(figsize=(40, 40))
-    ax = fig.add_axes([0, 0, 1, 1]) 
+    ax = fig.add_axes([0, 0, 1, 1])
     ax.axis('off')
 
     plt.imshow(img)
@@ -34,11 +35,12 @@
 
     fig.canvas.print_png(output_file, dpi=1800)
 
+
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     parser.add_argument('input_file', type=argparse.FileType('r'), help='original file')
     # output file should not be of type argparse.FileType('w') sine it is created immediately in this case which leads to an error in renaming
-    parser.add_argument('out_file_str', type=str, help='string of output file name') 
+    parser.add_argument('out_file_str', type=str, help='string of output file name')
     parser.add_argument('--tp', dest='input_tp_file', type=argparse.FileType('r'), help='input TP file')
     parser.add_argument('--fn', dest='input_fn_file', type=argparse.FileType('r'), help='input FN file')
     parser.add_argument('--fp', dest='input_fp_file', type=argparse.FileType('r'), help='input FP file')
@@ -46,14 +48,14 @@
     parser.add_argument('--circle_radius', dest='circle_radius', type=float, default=50, help='circle radius')
     args = parser.parse_args()
 
-    tp=None
+    tp = None
     if args.input_tp_file:
-        tp=args.input_tp_file.name
-    fn=None
+        tp = args.input_tp_file.name
+    fn = None
     if args.input_fn_file:
-        fn=args.input_fn_file.name
-    fp=None
+        fn = args.input_fn_file.name
+    fp = None
     if args.input_fp_file:
-        fp=args.input_fp_file.name
+        fp = args.input_fp_file.name
 
     detection_viz(args.input_file.name, args.out_file_str, tp=tp, fn=fn, fp=fp, stroke_size=args.thickness, circle_radius=args.circle_radius)

--- a/detection_viz.xml	Wed Dec 18 05:02:11 2019 -0500
+++ b/detection_viz.xml	Mon Nov 13 22:11:04 2023 +0000
@@ -1,5 +1,11 @@
-<tool id="ip_detection_viz" name="Detection Visualization" version="0.3"> 
-    <description>Detection Visualization</description>
+<tool id="ip_detection_viz" name="Visualize detections" version="0.3-2">
+    <description></description>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="0.14.2">scikit-image</requirement>
         <requirement type="package" version="3.0.2">matplotlib</requirement>
@@ -61,9 +67,15 @@
     <tests>
         <test>
             <param name="input" value="sample.png"/>
-            <param name="tp_option.display" value="false"/>
-            <param name="fn_option.display" value="false"/>
-            <param name="fp_option.display" value="false"/>
+            <conditional name="tp_option">
+                <param name="display" value="false"/>
+            </conditional>
+            <conditional name="fn_option">
+                <param name="display" value="false"/>
+            </conditional>
+            <conditional name="fp_option">
+                <param name="display" value="false"/>
+            </conditional>
             <output name="output" value="out.png" ftype="png"/>
         </test>
     </tests>