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annotate image_math.xml @ 0:33b2ca53a566 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
author imgteam
date Sat, 09 Mar 2024 22:04:19 +0000
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33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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1 <tool id="image_math" name="Process images using arithmetic expressions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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2 <description>with NumPy</description>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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3 <macros>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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4 <token name="@TOOL_VERSION@">1.26.4</token>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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5 <token name="@VERSION_SUFFIX@">0</token>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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6 </macros>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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7 <edam_operations>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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8 <edam_operation>operation_3443</edam_operation>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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9 </edam_operations>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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10 <requirements>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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11 <requirement type="package" version="1.26.4">numpy</requirement>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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12 <requirement type="package" version="0.22.0">scikit-image</requirement>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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13 </requirements>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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14 <command><![CDATA[
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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15
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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16 ## Inputs
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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17
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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18 python '$__tool_directory__/image_math.py'
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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19 --expression='$expression'
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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20 #for $item in $inputs:
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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21 --input='$item.name:$item.image'
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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22 #end for
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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23
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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24 ## Outputs
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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25
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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26 --output='./result.tiff'
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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27
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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28 ]]>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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29 </command>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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30 <inputs>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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31 <param argument="--expression" type="text" label="Expression" optional="false">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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32 <validator type="regex">^[a-zA-Z0-9-_\*\+ \(\)/]+$</validator>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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33 </param>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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34 <repeat name="inputs" title="Input images" min="1">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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35 <param name="image" type="data" format="png,tiff" label="Image" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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36 <param name="name" type="text" label="Variable for representation of the image within the expression" optional="false">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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37 <validator type="regex">^[a-zA-Z_][a-zA-Z0-9_]*$</validator>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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38 </param>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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39 </repeat>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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40 </inputs>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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41 <outputs>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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42 <data format="tiff" name="result" from_work_dir="result.tiff" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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43 </outputs>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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44 <tests>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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45 <!-- Multiplication with a scalar -->
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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46 <test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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47 <param name="expression" value="input1 * 2" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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48 <repeat name="inputs">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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49 <param name="image" value="input1.tiff" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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50 <param name="name" value="input1" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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51 </repeat>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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52 <output name="result" value="input1_times_2.tiff" ftype="tiff" compare="sim_size" delta="0" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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53 </test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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54 <!-- Unary negation operator -->
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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55 <test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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56 <param name="expression" value="-input1" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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57 <repeat name="inputs">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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58 <param name="image" value="input1.tiff" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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59 <param name="name" value="input1" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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60 </repeat>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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61 <output name="result" value="minus_input1.tiff" ftype="tiff" compare="sim_size" delta="0" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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62 </test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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63 <!-- Binary addition, neutral element, addition with scalar -->
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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64 <test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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65 <param name="expression" value="input1 + input2 + 1" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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66 <repeat name="inputs">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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67 <param name="image" value="input1.tiff" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
imgteam
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68 <param name="name" value="input1" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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69 </repeat>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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70 <repeat name="inputs">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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71 <param name="image" value="minus_input1.tiff" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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72 <param name="name" value="input2" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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73 </repeat>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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74 <output name="result" value="ones.tiff" ftype="tiff" compare="sim_size" delta="0" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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75 </test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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76 <!-- Parentheses -->
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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77 <test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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78 <param name="expression" value="(input1 + input2) / 2" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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79 <repeat name="inputs">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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80 <param name="image" value="input1.tiff" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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81 <param name="name" value="input1" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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82 </repeat>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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83 <repeat name="inputs">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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84 <param name="image" value="ones.tiff" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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85 <param name="name" value="input2" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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86 </repeat>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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87 <output name="result" value="half_of_input1_plus_one.tiff" ftype="tiff" compare="sim_size" delta="0" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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88 </test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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89 <!-- Abs -->
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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90 <test>
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91 <param name="expression" value="abs(input)" />
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92 <repeat name="inputs">
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93 <param name="image" value="input1.tiff" />
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94 <param name="name" value="input" />
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95 </repeat>
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96 <output name="result" value="input1_abs.tiff" ftype="tiff" compare="sim_size" delta="0" />
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97 </test>
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98 </tests>
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99 <help>
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100
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101 This tool processes images according to pixel-wise arithmetic expressions.
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102
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103 The supported pixel-wise expressions are:
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104
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105 - Addition, subtraction, multiplication, and division (``+``, ``-``, ``*``, ``/``)
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106 - Integer division (e.g., ``input // 2``)
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107 - Power (e.g., ``input ** 2``)
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108 - Negation (e.g., ``-input``)
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109 - Absolute values (e.g., ``abs(input)``)
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110 - Square root (e.g., ``sqrt(input)``)
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111 - Combinations of the above (also using parentheses)
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112
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113 Examples:
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114
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115 - **Negate an image.**
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116 Expression: ``-image``
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117 where ``image`` is an arbitrary input image.
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118
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119 - **Mean of two images.**
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120 Expression: ``(image1 + image2) / 2``
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121 where ``image1`` and `image2` are two arbitrary input images.
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122
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123 - **Perform division avoiding division-by-zero.**
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124 Expression: ``image1 / (abs(image2) + 1e-8)``
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125 where ``image1`` and `image2` are two arbitrary input images.
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126
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127 </help>
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128 <citations>
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129 <citation type="doi">10.1038/s41586-020-2649-2</citation>
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130 </citations>
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131 </tool>