annotate track_objects.py @ 6:a32c3f810ade draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author bgruening
date Sun, 05 Nov 2023 09:35:09 +0000
parents 91e03287f285
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
1 #!/usr/bin/env python
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
2
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
3 import argparse
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
4 import json
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
5
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
6 from cp_common_functions import (get_json_value,
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
7 get_pipeline_lines,
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
8 get_total_number_of_modules,
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
9 INDENTATION, update_module_count,
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
10 write_pipeline)
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
11
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
12 MODULE_NAME = "TrackObjects"
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
13 OUTPUT_FILENAME = "output.cppipe"
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
14
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
15
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
16 def build_header(module_name, module_number):
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
17 result = "|".join(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
18 [
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
19 f"{module_name}:[module_num:{module_number}",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
20 "svn_version:\\'Unknown\\'",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
21 "variable_revision_number:7",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
22 "show_window:True",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
23 "notes:\\x5B\\'Track the embryos across images using the Overlap method\\x3A tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.\\'\\x5D",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
24 "batch_state:array(\\x5B\\x5D, dtype=uint8)",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
25 "enabled:True",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
26 "wants_pause:False]\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
27 ]
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
28 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
29 return result
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
30
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
31
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
32 def build_main_block(input_params):
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
33 result = INDENTATION.join(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
34 [
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
35 f"{INDENTATION}Choose a tracking method:{get_json_value(input_params,'con_tracking_method.tracking_method')}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
36 f"Select the objects to track:{get_json_value(input_params,'object_to_track')}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
37 ]
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
38 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
39
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
40 tracking_method = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
41 input_params, "con_tracking_method.tracking_method"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
42 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
43
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
44 obj_measurement = "None" # default value
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
45 if tracking_method == "Measurements":
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
46 measurement_category = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
47 input_params,
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
48 "con_tracking_method.con_measurement_category.measurement_category",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
49 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
50 measurement = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
51 input_params, "con_tracking_method.con_measurement_category.measurement"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
52 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
53
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
54 if measurement_category == "Intensity" or measurement_category == "Location":
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
55 img_measure = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
56 input_params, "con_tracking_method.con_measurement_category.img_measure"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
57 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
58 obj_measurement = f"{measurement_category}_{measurement}_{img_measure}"
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
59 else:
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
60 obj_measurement = f"{measurement_category}_{measurement}"
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
61
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
62 result += INDENTATION.join(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
63 [
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
64 f"{INDENTATION}Select object measurement to use for tracking:{obj_measurement}\n"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
65 ]
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
66 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
67
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
68 if tracking_method == "LAP": # no max distance required, set default for pipeline
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
69 max_distance = 50
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
70 else:
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
71 max_distance = get_json_value(input_params, "con_tracking_method.max_distance")
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
72
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
73 result += INDENTATION.join(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
74 [f"{INDENTATION}Maximum pixel distance to consider matches:{max_distance}\n"]
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
75 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
76
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
77 display_option = get_json_value(input_params, "con_tracking_method.display_option")
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
78
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
79 output_img_name = "TrackedCells" # default value, required by cppipe regardless of its presence in UI
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
80 save = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
81 input_params, "con_tracking_method.con_save_coded_img.save_coded_img"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
82 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
83 if save == "Yes":
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
84 output_img_name = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
85 input_params, "con_tracking_method.con_save_coded_img.name_output_img"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
86 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
87
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
88 result += INDENTATION.join(
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
89 [
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
90 f"{INDENTATION}Select display option:{display_option}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
91 f"Save color-coded image?:{save}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
92 f"Name the output image:{output_img_name}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
93 ]
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
94 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
95
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
96 # LAP method default values
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
97 movement_model = "Both"
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
98 no_std = 3.0
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
99 radius_limit_max = 10.0
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
100 radius_limit_min = 2.0
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
101 radius = "2.0,10.0"
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
102 run_second = "Yes"
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
103 gap_closing = 40
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
104 split_alt = 40
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
105 merge_alt = 40
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
106 max_gap_displacement = 5
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
107 max_split = 50
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
108 max_merge = 50
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
109 max_temporal = 5
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
110 max_mitosis_dist = 40
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
111 mitosis_alt = 80
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
112
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
113 # LAP method
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
114 if tracking_method == "LAP":
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
115 movement_model = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
116 input_params, "con_tracking_method.movement_method"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
117 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
118 no_std = get_json_value(input_params, "con_tracking_method.no_std_radius")
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
119 radius_limit_max = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
120 input_params, "con_tracking_method.max_radius"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
121 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
122 radius_limit_min = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
123 input_params, "con_tracking_method.min_radius"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
124 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
125 radius = f"{radius_limit_min},{radius_limit_max}"
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
126
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
127 run_second = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
128 input_params, "con_tracking_method.con_second_lap.second_lap"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
129 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
130 if run_second == "Yes":
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
131 gap_closing = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
132 input_params, "con_tracking_method.con_second_lap.gap_closing"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
133 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
134 split_alt = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
135 input_params, "con_tracking_method.con_second_lap.split_alt"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
136 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
137 merge_alt = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
138 input_params, "con_tracking_method.con_second_lap.merge_alt"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
139 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
140 max_gap_displacement = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
141 input_params, "con_tracking_method.con_second_lap.max_gap_displacement"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
142 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
143 max_split = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
144 input_params, "con_tracking_method.con_second_lap.max_split"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
145 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
146 max_merge = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
147 input_params, "con_tracking_method.con_second_lap.max_merge"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
148 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
149 max_temporal = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
150 input_params, "con_tracking_method.con_second_lap.max_temporal"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
151 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
152 max_mitosis_dist = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
153 input_params, "con_tracking_method.con_second_lap.max_mitosis_distance"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
154 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
155 mitosis_alt = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
156 input_params, "con_tracking_method.con_second_lap.mitosis_alt"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
157 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
158
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
159 result += INDENTATION.join(
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
160 [
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
161 f"{INDENTATION}Select the movement model:{movement_model}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
162 f"Number of standard deviations for search radius:{no_std}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
163 f"Search radius limit, in pixel units (Min,Max):{radius}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
164 f"Run the second phase of the LAP algorithm?:{run_second}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
165 f"Gap closing cost:{gap_closing}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
166 f"Split alternative cost:{split_alt}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
167 f"Merge alternative cost:{merge_alt}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
168 f"Maximum gap displacement, in pixel units:{max_gap_displacement}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
169 f"Maximum split score:{max_split}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
170 f"Maximum merge score:{max_merge}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
171 f"Maximum temporal gap, in frames:{max_temporal}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
172 ]
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
173 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
174
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
175 # common section
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
176 filter_by_lifetime = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
177 input_params, "con_tracking_method.con_filter_by_lifetime.filter_by_lifetime"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
178 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
179 use_min = "Yes" # default
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
180 min_life = 1 # default
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
181 use_max = "No" # default
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
182 max_life = 100 # default
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
183
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
184 if filter_by_lifetime == "Yes":
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
185 use_min = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
186 input_params,
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
187 "con_tracking_method.con_filter_by_lifetime.con_use_min.use_min",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
188 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
189 if use_min == "Yes":
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
190 min_life = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
191 input_params,
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
192 "con_tracking_method.con_filter_by_lifetime.con_use_min.min_lifetime",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
193 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
194
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
195 use_max = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
196 input_params,
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
197 "con_tracking_method.con_filter_by_lifetime.con_use_max.use_max",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
198 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
199 if use_max == "Yes":
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
200 max_life = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
201 input_params,
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
202 "con_tracking_method.con_filter_by_lifetime.con_use_max.max_lifetime",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
203 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
204
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
205 result += INDENTATION.join(
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
206 [
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
207 f"{INDENTATION}Filter objects by lifetime?:{filter_by_lifetime}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
208 f"Filter using a minimum lifetime?:{use_min}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
209 f"Minimum lifetime:{min_life}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
210 f"Filter using a maximum lifetime?:{use_max}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
211 f"Maximum lifetime:{max_life}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
212 ]
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
213 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
214
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
215 # print 2 leftover from LAP
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
216 result += INDENTATION.join(
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
217 [
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
218 f"{INDENTATION}Mitosis alternative cost:{mitosis_alt}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
219 f"Maximum mitosis distance, in pixel units:{max_mitosis_dist}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
220 ]
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
221 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
222
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
223 # Follow Neighbors
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
224 # defaults
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
225 avg_cell_diameter = 35.0
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
226 use_adv = "No"
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
227 cost_of_cell = 15.0
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
228 weight_of_area_diff = 25.0
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
229
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
230 if tracking_method == "Follow Neighbors":
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
231 avg_cell_diameter = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
232 input_params, "con_tracking_method.avg_diameter"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
233 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
234 use_adv = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
235 input_params, "con_tracking_method.con_adv_parameter.adv_parameter"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
236 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
237 if use_adv == "Yes":
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
238 cost_of_cell = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
239 input_params, "con_tracking_method.con_adv_parameter.cost"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
240 )
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
241 weight_of_area_diff = get_json_value(
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
242 input_params, "con_tracking_method.con_adv_parameter.weight"
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
243 )
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
244
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
245 result += INDENTATION.join(
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
246 [
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
247 f"{INDENTATION}Average cell diameter in pixels:{avg_cell_diameter}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
248 f"Use advanced configuration parameters:{use_adv}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
249 f"Cost of cell to empty matching:{cost_of_cell}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
250 f"Weight of area difference in function matching cost:{weight_of_area_diff}\n",
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
251 ]
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
252 )
5
91e03287f285 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
bgruening
parents: 4
diff changeset
253 result = result.rstrip("\n")
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
254 return result
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
255
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
256
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
257 if __name__ == "__main__":
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
258 parser = argparse.ArgumentParser()
6
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
259 parser.add_argument("-p", "--pipeline", help="CellProfiler pipeline")
a32c3f810ade planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
bgruening
parents: 5
diff changeset
260 parser.add_argument("-i", "--inputs", help="JSON inputs from Galaxy")
4
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
261 args = parser.parse_args()
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
262
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
263 pipeline_lines = get_pipeline_lines(args.pipeline)
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
264 inputs_galaxy = json.load(open(args.inputs, "r"))
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
265
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
266 current_module_num = get_total_number_of_modules(pipeline_lines)
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
267 current_module_num += 1
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
268 pipeline_lines = update_module_count(pipeline_lines, current_module_num)
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
269
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
270 header_block = build_header(MODULE_NAME, current_module_num)
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
271 main_block = build_main_block(inputs_galaxy)
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
272
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
273 module_pipeline = f"\n{header_block}{main_block}\n"
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
274 pipeline_lines.append(module_pipeline)
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
275
20dbb1f7ec7b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
parents:
diff changeset
276 write_pipeline(OUTPUT_FILENAME, pipeline_lines)