Mercurial > repos > imgteam > imagej2_analyze_particles_binary

annotate imagej2_analyze_particles_binary.xml @ 0:cb022577a9f1 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 16:53:22 -0400
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0
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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1 <?xml version='1.0' encoding='UTF-8'?>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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2 <tool id="imagej2_analyze_particles_binary" name="Analyze particles" version="@WRAPPER_VERSION@.0">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 <description>of binary image</description>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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4 <macros>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 <import>imagej2_macros.xml</import>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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6 </macros>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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7 <expand macro="fiji_requirements" />
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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8 <command>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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9 <![CDATA[
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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10 python $__tool_directory__/imagej2_analyze_particles_binary.py
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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11 --input "$input"
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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12 --input_datatype $input.ext
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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13 --black_background $black_background
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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14 --size "$size"
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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15 --circularity_min $circularity_min
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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16 --circularity_max $circularity_max
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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17 --show $show
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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18 --exclude_edges $exclude_edges
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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19 --include_holes $include_holes
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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20 --jython_script $__tool_directory__/imagej2_analyze_particles_binary_jython_script.py
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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21 #if str($show) == 'Nothing':
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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22 --display_results "yes"
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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23 --all_results "yes"
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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24 #else:
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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25 --display_results $display_results_cond.display_results
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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26 --all_results $display_results_cond.all_results
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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27 --output_datatype $output.ext
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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28 --output "$output"
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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29 #end if
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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30 --results "$results"
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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31 ]]>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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32 </command>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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33 <inputs>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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34 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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35 <expand macro="black_background_param" />
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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36 <param name="size" type="text" value="0-Infinity" label="Size (pixel^2)" help="Enter a single value and particles smaller than that value will be ignored."/>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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37 <param name="circularity_min" type="float" value="0.0" label="Circularity minimum" help="Values from 0.0 to 1.0, but less than maximum">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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38 <validator type="in_range" min="0" max="1"/>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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39 </param>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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40 <param name="circularity_max" type="float" value="1.0" label="Circularity maximum" help="Values from 0.0 to 1.0, but greater than minimum">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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41 <validator type="in_range" min="0" max="1"/>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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42 </param>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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43 <param name="show" type="select" label="Show" help="Selecting Nothing will display results, but no image.">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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44 <option value="Outlines" selected="True">Outlines</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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45 <option value="Bare_Outlines">Bare Outlines</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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46 <option value="Ellipses">Ellipses</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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47 <option value="Masks">Masks</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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48 <option value="Count_Masks">Count Masks</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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49 <option value="Nothing">Nothing</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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50 </param>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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51 <conditional name="display_results_cond">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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52 <param name="display_results" type="select" label="Display results">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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53 <option value="no" selected="True">No</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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54 <option value="yes">Yes</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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55 </param>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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56 <when value="no">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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57 <param name="all_results" type="hidden" value="no"/>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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58 </when>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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59 <when value="yes">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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60 <param name="all_results" type="select" label="All results?" help="If no, only summary displayed.">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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61 <option value="yes" selected="True">Yes</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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62 <option value="no">No</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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63 </param>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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64 </when>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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65 </conditional>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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66 <param name="exclude_edges" type="select" label="Exclude on edges?">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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67 <option value="no" selected="True">No</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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68 <option value="yes">Yes</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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69 </param>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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70 <param name="include_holes" type="select" label="Include holes?">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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71 <option value="no" selected="True">No</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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72 <option value="yes">Yes</option>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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73 </param>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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74 </inputs>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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75 <outputs>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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76 <data name="output" format_source="input" label="${tool.name} on ${on_string}">
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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77 <filter>show != "Nothing"</filter>
cb022577a9f1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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78 </data>
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79 <data format="tabular" name="results" label="${tool.name} on ${on_string}: Results">
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80 <filter>show == "Nothing" or display_results_cond['display_results'] == "yes"</filter>
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81 </data>
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="input" value="blobs_watershed_binary.gif" />
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86 <param name="show" value="Nothing" />
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87 <output name="output" file="analyze_particles_nothing.tabular" />
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88 </test>
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89 <test>
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90 <param name="input" value="blobs_watershed_binary.gif" />
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91 <param name="show" value="Outlines" />
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92 <output name="output" file="analyze_particles_outlines.gif" compare="sim_size" />
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93 </test>
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94 <test>
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95 <param name="input" value="blobs_watershed_binary.gif" />
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96 <param name="show" value="Masks" />
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97 <param name="exclude_edges" value="yes" />
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98 <param name="include_holes" value="yes" />
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99 <output name="output" file="analyze_particles_masks.gif" compare="sim_size" />
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100 </test>
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101 </tests>
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102 <help>
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103 .. class:: warningmark
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104
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105 @requires_binary_input@
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106
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107 **What it does**
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108
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109 <![CDATA[
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110 Counts and measures objects in binary or thresholded images. It works by scanning the image until
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111 it finds the edge of an object. It then outlines the object, measures it, fills it to make it
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112 invisible, then resumes scanning until it reaches the end of the image. Features of thresholded
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113 images can be extracted by specifying suitable **Size** and **Circularity** ranges and/or by choosing
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114 if particles should be traced by their outer edge or by flood filling.
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115
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116 - **Size** - Particles with size (area) outside the range specified in this field are ignored. Values may range between 0 and ‘Infinity’. Enter a single value and particles smaller than that value will be ignored.
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117 - **Cicularity** - Particles with size circularity values outside the range specified in the min/max fields are also ignored.
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118 - **Show: Nothing** - No image will be generated, but **Display Results** will be set to Yes. Note that the particle analyzer will display a blank image when the count of detected particles is zero and **Show** is not **Nothing**.
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119 - **Show: Outlines** - Generates an 8-bit image containing numbered outlines of the measured particles (gray levels: Outlines: 0; Labels: 1; Background: 255).
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120 - **Show: Bare Outlines** - Generates an 8-bit image containing simple outlines of the measured particles without labels (graylevels: Outlines: 0; Background: 255).
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121 - **Show: Ellipses** - Generates an 8-bit image containing the best fit ellipse of each measured particle (gray levels: Ellipses: 0; Background: 255).
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122 - **Show: Masks** - Generates an 8-bit image containing filled outlines of the measured particles (gray levels: Masks: 0; Background: 255).
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123 - **Show: Count Masks** - Generates a 16-bit image containing filled outlines of the measured particles painted with a grayscale value corresponding to the particle number.
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124 - **Display Results** - If Yes, the measurements for each particle will be generated.
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125 - **All results** - If No, results will be restricted to the particle count, total particle area, average particle size, and area fraction.
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126 - **Exclude on Edges** - If Yes, particles touching the edge of the image will be ignored.
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127 - **Include Holes** - If Yes, interior holes will be included (set to No to exclude interior holes and to measure particles enclosed by other particles).
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128 ]]>
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129
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130 </help>
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131 <expand macro="fiji_headless_citations" />
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132 </tool>