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annotate spot_detection_2d.xml @ 3:b47931e176c3 draft

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"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit ae389b10be46633407effcc6856167f6e8bb2122"
author imgteam
date Sat, 09 Apr 2022 12:45:51 +0000
parents 2f2d46f89418
children d77f71572fc4
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b47931e176c3 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit ae389b10be46633407effcc6856167f6e8bb2122"
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1 <tool id="ip_spot_detection_2d" name="Spot Detection" version="0.0.3" profile="20.05">
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2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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2 <description>in a 2D image (sequence)</description>
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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3 <requirements>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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4 <requirement type="package" version="2.9.0">imageio</requirement>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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5 <requirement type="package" version="1.20.2">numpy</requirement>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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6 <requirement type="package" version="1.2.4">pandas</requirement>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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7 <requirement type="package" version="0.18.1">scikit-image</requirement>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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8 </requirements>
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2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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9 <command detect_errors="aggressive">
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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10 <![CDATA[
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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11 python '$__tool_directory__/spot_detection_2d.py'
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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12 '$fn_in'
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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13 '$fn_out'
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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14 '$frame_1st'
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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15 '$frame_end'
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16 '$filter'
2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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17 '$ssig'
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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18 '$thres'
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19 '$typ_intens'
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20 '$bndy'
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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21 ]]>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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22 </command>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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23 <inputs>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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24 <param name="fn_in" type="data" format="tiff" label="Image sequence (stack)" />
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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25 <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" />
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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26 <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
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2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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27 <param name="filter" type="select" label="Choose a detection filter">
2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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28 <option value="Gauss" selected="True">Gaussian</option>
2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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29 <option value="LoG">Laplacian-of-Gaussian, LoG (more accurate when spots have similar sizes)</option>
2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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30 </param>
2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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31 <param name="ssig" type="float" value="1.0" min="0.5" max="10" label="Sigma of the Gaussian (for noise suppression)" />
2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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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" />
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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33 <param name="typ_intens" type="select" label="How to measure the intensities">
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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34 <option value="smoothed" selected="True">Smoothed</option>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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35 <option value="robust">Robust</option>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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36 </param>
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2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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37 <param name="bndy" type="integer" value="10" min="0" max="50" label="Width (in pixel) of image boundaries where spots will be ignored" />
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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38 </inputs>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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39 <outputs>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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40 <data format="tabular" name="fn_out" />
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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41 </outputs>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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42 <tests>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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43 <test>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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44 <param name="fn_in" value="test_img1.tif"/>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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45 <param name="frame_1st" value="1"/>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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46 <param name="frame_end" value="0"/>
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47 <param name="filter" value="Gauss"/>
2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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48 <param name="ssig" value="1"/>
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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49 <param name="thres" value="10"/>
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50 <param name="typ_intens" value="smoothed"/>
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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51 <param name="bndy" value="10"/>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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52 <output name="fn_out" value="spots_detected.tsv" ftype="tabular" />
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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53 </test>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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54 </tests>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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55 <help>
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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56 **What it does**
ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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57
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2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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58 This tool detects spots and measures the intensities in a 2D image (sequence).
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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59 </help>
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2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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60 <citations>
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b47931e176c3 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit ae389b10be46633407effcc6856167f6e8bb2122"
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61 <citation type="doi">10.1097/j.pain.0000000000002642</citation>
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2f2d46f89418 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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62 </citations>
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ba44bc2a0928 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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63 </tool>