Mercurial > repos > imgteam > spot_detection_2d

annotate spot_detection_2d.xml @ 4:14f9986800fa draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:12:30 +0000
parents a9972c993bed
children e8c9e104e109
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14f9986800fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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1 <tool id="ip_spot_detection_2d" name="Perform 2D spot detection" version="0.0.3-2" profile="20.05">
14f9986800fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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2 <description></description>
14f9986800fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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3 <edam_operations>
14f9986800fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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4 <edam_operation>operation_3443</edam_operation>
14f9986800fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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5 </edam_operations>
14f9986800fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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6 <xrefs>
14f9986800fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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7 <xref type="bio.tools">galaxy_image_analysis</xref>
14f9986800fa planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
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8 </xrefs>
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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9 <requirements>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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10 <requirement type="package" version="2.9.0">imageio</requirement>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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11 <requirement type="package" version="1.20.2">numpy</requirement>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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12 <requirement type="package" version="1.2.4">pandas</requirement>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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13 <requirement type="package" version="0.18.1">scikit-image</requirement>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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14 </requirements>
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859dd1c11ac0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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15 <command detect_errors="aggressive">
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d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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16 <![CDATA[
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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17 python '$__tool_directory__/spot_detection_2d.py'
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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18 '$fn_in'
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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19 '$fn_out'
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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20 '$frame_1st'
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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21 '$frame_end'
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22 '$filter'
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23 '$ssig'
0
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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24 '$thres'
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25 '$typ_intens'
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d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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26 '$bndy'
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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27 ]]>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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28 </command>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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29 <inputs>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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30 <param name="fn_in" type="data" format="tiff" label="Image sequence (stack)" />
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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31 <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" />
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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32 <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
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859dd1c11ac0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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33 <param name="filter" type="select" label="Choose a detection filter">
859dd1c11ac0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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34 <option value="Gauss" selected="True">Gaussian</option>
859dd1c11ac0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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35 <option value="LoG">Laplacian-of-Gaussian, LoG (more accurate when spots have similar sizes)</option>
859dd1c11ac0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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36 </param>
859dd1c11ac0 "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="ssig" type="float" value="1.0" min="0.5" max="10" label="Sigma of the Gaussian (for noise suppression)" />
859dd1c11ac0 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 9f103372d66ae7e3c5c385bd444b2a80e51cdae6"
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38 <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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39 <param name="typ_intens" type="select" label="How to measure the intensities">
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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40 <option value="smoothed" selected="True">Smoothed</option>
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41 <option value="robust">Robust</option>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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42 </param>
1
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43 <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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d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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44 </inputs>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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45 <outputs>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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46 <data format="tabular" name="fn_out" />
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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47 </outputs>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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48 <tests>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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49 <test>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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50 <param name="fn_in" value="test_img1.tif"/>
d78372040976 "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="frame_1st" value="1"/>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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52 <param name="frame_end" value="0"/>
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53 <param name="filter" value="Gauss"/>
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54 <param name="ssig" value="1"/>
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55 <param name="thres" value="10"/>
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56 <param name="typ_intens" value="smoothed"/>
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57 <param name="bndy" value="10"/>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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58 <output name="fn_out" value="spots_detected.tsv" ftype="tabular" />
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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59 </test>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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60 </tests>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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61 <help>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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62 **What it does**
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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63
1
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64 This tool detects spots and measures the intensities in a 2D image (sequence).
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d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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65 </help>
1
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66 <citations>
3
a9972c993bed "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit ae389b10be46633407effcc6856167f6e8bb2122"
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67 <citation type="doi">10.1097/j.pain.0000000000002642</citation>
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68 </citations>
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69 </tool>