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comparison spot_detection_2d.xml @ 0:d78372040976 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
author imgteam
date Wed, 21 Jul 2021 19:59:00 +0000
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1 <tool id="ip_spot_detection_2d" name="Spot Detection" version="0.0.1" profile="20.05">
2 <description>based on local intensity maxima</description>
3 <requirements>
4 <requirement type="package" version="2.9.0">imageio</requirement>
5 <requirement type="package" version="1.20.2">numpy</requirement>
6 <requirement type="package" version="1.2.4">pandas</requirement>
7 <requirement type="package" version="0.18.1">scikit-image</requirement>
8 </requirements>
9 <command>
10 <![CDATA[
11 python '$__tool_directory__/spot_detection_2d.py'
12 '$fn_in'
13 '$fn_out'
14 '$frame_1st'
15 '$frame_end'
16 '$typ_intens'
17 '$thres'
18 '$ssig'
19 '$bndy'
20 ]]>
21 </command>
22 <inputs>
23 <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_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
26 <param name="typ_intens" type="select" label="How to measure the intensities">
27 <option value="smoothed" selected="True">Smoothed</option>
28 <option value="robust">Robust</option>
29 </param>
30 <param name="thres" type="float" value="10" label="Percentage of the global maximal intensity as the threshold for candidate spots" />
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>
34 <outputs>
35 <data format="tabular" name="fn_out" />
36 </outputs>
37 <tests>
38 <test>
39 <param name="fn_in" value="test_img1.tif"/>
40 <param name="frame_1st" value="1"/>
41 <param name="frame_end" value="0"/>
42 <param name="typ_intens" value="smoothed"/>
43 <param name="thres" value="10"/>
44 <param name="ssig" value="1"/>
45 <param name="bndy" value="10"/>
46 <output name="fn_out" value="spots_detected.tsv" ftype="tabular" />
47 </test>
48 </tests>
49 <help>
50 **What it does**
51
52 This tool detects spots and measures the intensities in a 2D image sequence based on local intensity maxima.
53 </help>
54 </tool>