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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:07:20 +0000
parents 182994b12622
children
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91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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1 <tool id="imagej2_binary_to_edm" name="Convert binary image to EDM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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182994b12622 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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2 <description>with ImageJ2</description>
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3 <macros>
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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4 <import>imagej2_macros.xml</import>
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 </macros>
2
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6 <edam_operations>
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7 <edam_operation>operation_3443</edam_operation>
182994b12622 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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8 </edam_operations>
182994b12622 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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9 <xrefs>
182994b12622 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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10 <xref type="bio.tools">imagej</xref>
182994b12622 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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11 <xref type="biii">imagej2</xref>
182994b12622 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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12 </xrefs>
1
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13 <expand macro="fiji_requirements"/>
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14 <command detect_errors="exit_code"><![CDATA[
33f6b1f921e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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15 #import os
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16 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
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91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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17 #set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
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18 ln -s '$input.file_name' '$input_with_ext' &&
33f6b1f921e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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19 #set output_filename = '.'.join(['output', $input.ext])
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20 touch '$output_filename' &&
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21 ImageJ --ij2 --headless --debug
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22 --jython '$__tool_directory__/imagej2_binary_to_edm_jython_script.py'
33f6b1f921e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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23 '$input_with_ext'
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24 $iterations
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25 $count
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26 '$black_background'
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27 '$pad_edges_when_eroding'
33f6b1f921e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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28 '$output_filename'
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29 '$input.ext'
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30 && mv '$output_filename' '$output';
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31 ]]></command>
0
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32 <inputs>
1
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33 <expand macro="param_input"/>
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34 <expand macro="make_binary_params"/>
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35 </inputs>
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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36 <outputs>
1
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37 <data name="output" format_source="input"/>
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38 </outputs>
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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39 <tests>
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40 <test>
1
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41 <param name="input" value="blobs.gif"/>
33f6b1f921e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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42 <param name="iterations" value="1"/>
33f6b1f921e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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43 <param name="count" value="1"/>
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91b8f4730a93 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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44 <output name="output" file="blobs_edm.gif" compare="image_diff" metric="iou" />
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45 </test>
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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46 <test>
1
33f6b1f921e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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47 <param name="input" value="blobs.gif"/>
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48 <param name="iterations" value="10"/>
33f6b1f921e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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49 <param name="count" value="3"/>
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50 <param name="black_background" value="yes"/>
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51 <param name="pad_edges_when_eroding" value="yes"/>
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52 <output name="output" file="blobs_black_edm.gif" compare="image_diff" metric="iou" />
0
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53 </test>
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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54 </tests>
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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55 <help>
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56
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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57 .. class:: warningmark
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58
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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59 @requires_binary_input@
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60
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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61 **What it does**
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62
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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63 <![CDATA[
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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64 Converts a binary image into an 8-bit grayscale Euclidean Distance Map (EDM). Each foreground
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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65 (nonzero) pixel in the binary image is assigned a value equal to its distance from the nearest
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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66 background (zero) pixel.
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67
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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68 - **Iterations** - Specifies the number of times erosion, dilation, opening, and closing are performed.
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69 - **Count** - Specifies the number of adjacent background pixels necessary before a pixel is removed from the edge of an object during erosion and the number of adjacent foreground pixels necessary before a pixel is added to the edge of an object during dilation.
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70 - **Black background** - If **Yes**, binary images will be created without using an inverted LUT and an assumption that the input image contains white objects on a black background will be made.
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71 - **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image.
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72
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73 ]]>
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74
f62303e87275 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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75 </help>
1
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76 <expand macro="fiji_headless_citations"/>
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77 </tool>