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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 16:37:50 -0400
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308625693e9a "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'?>
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2 <tool id="imagej2_binary_to_edm" name="Convert binary image to EDM" version="@WRAPPER_VERSION@.0">
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3 <description>(Euclidean Distance Map)</description>
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4 <macros>
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5 <import>imagej2_macros.xml</import>
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6 </macros>
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7 <expand macro="fiji_requirements" />
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8 <command>
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9 <![CDATA[
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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10 python $__tool_directory__/imagej2_binary_to_edm.py
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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11 --input "$input"
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12 --input_datatype $input.ext
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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13 @make_binary_args@
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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14 --jython_script $__tool_directory__/imagej2_binary_to_edm_jython_script.py
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15 --output_datatype $output.ext
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16 --output "$output"
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
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21 <expand macro="make_binary_params" />
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22 </inputs>
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23 <outputs>
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24 <data name="output" format_source="input" label="${tool.name} on ${on_string}"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input" value="blobs.gif" />
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29 <param name="iterations" value="1" />
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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30 <param name="count" value="1" />
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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31 <output name="output" file="blobs_edm.gif" compare="sim_size" />
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32 </test>
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33 <test>
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34 <param name="input" value="blobs.gif" />
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35 <param name="iterations" value="10" />
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36 <param name="count" value="3" />
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37 <param name="black_background" value="yes" />
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38 <param name="pad_edges_when_eroding" value="yes" />
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39 <output name="output" file="blobs_black_edm.gif" compare="sim_size" />
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40 </test>
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41 </tests>
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42 <help>
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43
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44 .. class:: warningmark
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45
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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46 @requires_binary_input@
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47
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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48 **What it does**
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49
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50 <![CDATA[
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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51 Converts a binary image into an 8-bit grayscale Euclidean Distance Map (EDM). Each foreground
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52 (nonzero) pixel in the binary image is assigned a value equal to its distance from the nearest
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53 background (zero) pixel.
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54
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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55 - **Iterations** - Specifies the number of times erosion, dilation, opening, and closing are performed.
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56 - **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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57 - **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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58 - **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image.
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59
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60 ]]>
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61
308625693e9a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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62 </help>
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63 <expand macro="fiji_headless_citations" />
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64 </tool>