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annotate imagej2_make_binary.xml @ 0:baa308e2533a draft

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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 17:07:31 -0400
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children 6e8be21a505c
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baa308e2533a "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'?>
baa308e2533a "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_make_binary" name="Convert to binary" version="@WRAPPER_VERSION@.0">
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 <description>(black and white)</description>
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4 <macros>
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5 <import>imagej2_macros.xml</import>
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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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[
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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10 python $__tool_directory__/imagej2_make_binary.py
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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11 --input "$input"
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12 --input_datatype $input.ext
baa308e2533a "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@
baa308e2533a "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_make_binary_jython_script.py
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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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" />
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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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}"/>
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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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="clown.jpg" />
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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29 <param name="input_datatype" value="jpg" />
baa308e2533a "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="iterations" value="1" />
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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31 <param name="count" value="1" />
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32 <param name="black_background" value="no" />
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33 <param name="pad_edges_when_eroding" value="no" />
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34 <param name="output_datatype" value="jpg" />
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35 <output name="output" file="clown_binary.jpg" compare="sim_size" />
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36 </test>
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37 </tests>
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38 <help>
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39 **What it does**
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40
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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41 <![CDATA[
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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42 Converts an image into a binary (black and white) image by analyzing the histogram of
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43 the entire image and setting an automatic threshold level to create the binary image.
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44
baa308e2533a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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45 - **Iterations** - Specifies the number of times erosion, dilation, opening, and closing are performed.
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46 - **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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47 - **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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48 - **Pad edges when eroding** - If **Yes**, eroding does not erode from the edges of the image.
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49
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50 ]]>
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51
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52 </help>
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53 <expand macro="fiji_headless_citations" />
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54 </tool>