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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 16:00:05 +0000
parents aeae7e29d525
children
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29aca8eebdaa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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1 <tool id="imagej2_watershed_binary" name="Perform segmentation using watershed transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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aeae7e29d525 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>
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4 <import>imagej2_macros.xml</import>
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5 </macros>
2
aeae7e29d525 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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6 <edam_operations>
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7 <edam_operation>operation_3443</edam_operation>
aeae7e29d525 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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8 </edam_operations>
aeae7e29d525 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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9 <xrefs>
aeae7e29d525 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>
aeae7e29d525 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>
aeae7e29d525 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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12 </xrefs>
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13 <expand macro="fiji_requirements"/>
5b154339fd90 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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14 <command detect_errors="exit_code"><![CDATA[
5b154339fd90 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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15 #import os
5b154339fd90 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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16 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
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29aca8eebdaa 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' &&
5b154339fd90 "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', $input.ext])
5b154339fd90 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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20 touch '$output_filename' &&
5b154339fd90 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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21 ImageJ --ij2 --headless --debug
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22 --jython '$__tool_directory__/imagej2_watershed_binary_jython_script.py'
5b154339fd90 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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23 '$input_with_ext'
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24 '$black_background'
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25 '$output_filename'
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26 '$input.ext'
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29aca8eebdaa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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27 && mv '$output_filename' '$output';
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28 ]]></command>
0
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29 <inputs>
1
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30 <expand macro="param_input"/>
5b154339fd90 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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31 <expand macro="black_background_param"/>
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32 </inputs>
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33 <outputs>
1
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34 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
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35 </outputs>
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36 <tests>
b143159845b4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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37 <test>
1
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38 <param name="input" value="blobs.gif"/>
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29aca8eebdaa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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39 <output name="output" file="blobs_watershed_binary.gif" compare="image_diff"/>
29aca8eebdaa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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40 </test>
29aca8eebdaa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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41 <test>
29aca8eebdaa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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42 <param name="input" value="confocal-series-first-channel_threshold_default.tiff"/>
29aca8eebdaa planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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43 <param name="black_background" value="yes"/>
29aca8eebdaa 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="confocal-series-first-channel_default_threshold_watershed.tiff" compare="sim_size"/>
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45 </test>
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46 </tests>
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47 <help>
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48 .. class:: warningmark
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49
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50 @requires_binary_input@
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51
b143159845b4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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52 **What it does**
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53
b143159845b4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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54 <![CDATA[
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55 Watershed segmentation is a way of automatically separating or cutting apart particles that touch.
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56 It first calculates the Euclidian distance map (EDM) and finds the ultimate eroded points (UEPs).
b143159845b4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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57 It then dilates each of the UEPs (the peaks or local maxima of the EDM) as far as possible — either
b143159845b4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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58 until the edge of the particle is reached, or the edge touches a region of another (growing) UEP.
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59 Watershed segmentation works best for smooth convex objects that don’t overlap too much.
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60 ]]>
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61
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62 </help>
1
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63 <expand macro="fiji_headless_citations"/>
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64 </tool>