Mercurial > repos > imgteam > spot_detection_2d
comparison spot_detection_2d.xml @ 1:859dd1c11ac0 draft
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
author | imgteam |
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date | Sat, 19 Feb 2022 20:43:29 +0000 |
parents | d78372040976 |
children | a9972c993bed |
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0:d78372040976 | 1:859dd1c11ac0 |
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1 <tool id="ip_spot_detection_2d" name="Spot Detection" version="0.0.1" profile="20.05"> | 1 <tool id="ip_spot_detection_2d" name="Spot Detection" version="0.0.2" profile="20.05"> |
2 <description>based on local intensity maxima</description> | 2 <description>in a 2D image (sequence)</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="2.9.0">imageio</requirement> | 4 <requirement type="package" version="2.9.0">imageio</requirement> |
5 <requirement type="package" version="1.20.2">numpy</requirement> | 5 <requirement type="package" version="1.20.2">numpy</requirement> |
6 <requirement type="package" version="1.2.4">pandas</requirement> | 6 <requirement type="package" version="1.2.4">pandas</requirement> |
7 <requirement type="package" version="0.18.1">scikit-image</requirement> | 7 <requirement type="package" version="0.18.1">scikit-image</requirement> |
8 </requirements> | 8 </requirements> |
9 <command> | 9 <command detect_errors="aggressive"> |
10 <![CDATA[ | 10 <![CDATA[ |
11 python '$__tool_directory__/spot_detection_2d.py' | 11 python '$__tool_directory__/spot_detection_2d.py' |
12 '$fn_in' | 12 '$fn_in' |
13 '$fn_out' | 13 '$fn_out' |
14 '$frame_1st' | 14 '$frame_1st' |
15 '$frame_end' | 15 '$frame_end' |
16 '$filter' | |
17 '$ssig' | |
18 '$thres' | |
16 '$typ_intens' | 19 '$typ_intens' |
17 '$thres' | |
18 '$ssig' | |
19 '$bndy' | 20 '$bndy' |
20 ]]> | 21 ]]> |
21 </command> | 22 </command> |
22 <inputs> | 23 <inputs> |
23 <param name="fn_in" type="data" format="tiff" label="Image sequence (stack)" /> | 24 <param name="fn_in" type="data" format="tiff" label="Image sequence (stack)" /> |
24 <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" /> | 25 <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" /> |
25 <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" /> | 26 <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" /> |
27 <param name="filter" type="select" label="Choose a detection filter"> | |
28 <option value="Gauss" selected="True">Gaussian</option> | |
29 <option value="LoG">Laplacian-of-Gaussian, LoG (more accurate when spots have similar sizes)</option> | |
30 </param> | |
31 <param name="ssig" type="float" value="1.0" min="0.5" max="10" label="Sigma of the Gaussian (for noise suppression)" /> | |
32 <param name="thres" type="float" value="10.0" min="0" max="100" label="Percentage of the global maximal as the threshold for candidate spots" /> | |
26 <param name="typ_intens" type="select" label="How to measure the intensities"> | 33 <param name="typ_intens" type="select" label="How to measure the intensities"> |
27 <option value="smoothed" selected="True">Smoothed</option> | 34 <option value="smoothed" selected="True">Smoothed</option> |
28 <option value="robust">Robust</option> | 35 <option value="robust">Robust</option> |
29 </param> | 36 </param> |
30 <param name="thres" type="float" value="10" label="Percentage of the global maximal intensity as the threshold for candidate spots" /> | 37 <param name="bndy" type="integer" value="10" min="0" max="50" label="Width (in pixel) of image boundaries where spots will be ignored" /> |
31 <param name="ssig" type="float" value="1" label="Sigma of the Gaussian filter for noise suppression" /> | |
32 <param name="bndy" type="integer" value="10" label="Number of pixels (Spots within n-pixel image boundaries will be ignored)" /> | |
33 </inputs> | 38 </inputs> |
34 <outputs> | 39 <outputs> |
35 <data format="tabular" name="fn_out" /> | 40 <data format="tabular" name="fn_out" /> |
36 </outputs> | 41 </outputs> |
37 <tests> | 42 <tests> |
38 <test> | 43 <test> |
39 <param name="fn_in" value="test_img1.tif"/> | 44 <param name="fn_in" value="test_img1.tif"/> |
40 <param name="frame_1st" value="1"/> | 45 <param name="frame_1st" value="1"/> |
41 <param name="frame_end" value="0"/> | 46 <param name="frame_end" value="0"/> |
47 <param name="filter" value="Gauss"/> | |
48 <param name="ssig" value="1"/> | |
49 <param name="thres" value="10"/> | |
42 <param name="typ_intens" value="smoothed"/> | 50 <param name="typ_intens" value="smoothed"/> |
43 <param name="thres" value="10"/> | |
44 <param name="ssig" value="1"/> | |
45 <param name="bndy" value="10"/> | 51 <param name="bndy" value="10"/> |
46 <output name="fn_out" value="spots_detected.tsv" ftype="tabular" /> | 52 <output name="fn_out" value="spots_detected.tsv" ftype="tabular" /> |
47 </test> | 53 </test> |
48 </tests> | 54 </tests> |
49 <help> | 55 <help> |
50 **What it does** | 56 **What it does** |
51 | 57 |
52 This tool detects spots and measures the intensities in a 2D image sequence based on local intensity maxima. | 58 This tool detects spots and measures the intensities in a 2D image (sequence). |
53 </help> | 59 </help> |
60 <citations> | |
61 </citations> | |
54 </tool> | 62 </tool> |