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annotate image_math.xml @ 1:f8b7770cbca5 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:25:35 +0000
parents 33b2ca53a566
children 48fa3ac55df2
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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
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2 <description>with NumPy</description>
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3 <macros>
1
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4 <import>creators.xml</import>
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5 <import>tests.xml</import>
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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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6 <token name="@TOOL_VERSION@">1.26.4</token>
1
f8b7770cbca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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7 <token name="@VERSION_SUFFIX@">1</token>
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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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8 </macros>
1
f8b7770cbca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit c045f067a57e8308308cf6329060c7ccd3fc372f
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9 <creator>
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10 <expand macro="creators/bmcv"/>
f8b7770cbca5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit c045f067a57e8308308cf6329060c7ccd3fc372f
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11 </creator>
0
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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12 <edam_operations>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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13 <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
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14 </edam_operations>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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15 <requirements>
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16 <requirement type="package" version="@TOOL_VERSION@">numpy</requirement>
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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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17 <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
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18 </requirements>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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19 <command><![CDATA[
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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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21 ## Inputs
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22
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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23 python '$__tool_directory__/image_math.py'
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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24 --expression='$expression'
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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25 #for $item in $inputs:
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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26 --input='$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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27 #end for
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28
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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29 ## Outputs
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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30
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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31 --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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32
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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33 ]]>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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34 </command>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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35 <inputs>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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36 <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
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37 <validator type="regex">^[a-zA-Z0-9-_\*\+ \(\)/]+$</validator>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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38 </param>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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39 <repeat name="inputs" title="Input images" min="1">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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40 <param name="image" type="data" format="png,tiff" label="Image" />
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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41 <param name="name" type="text" label="Variable for representation of the image within the expression" optional="false">
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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42 <validator type="regex">^[a-zA-Z_][a-zA-Z0-9_]*$</validator>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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43 </param>
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44 </repeat>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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45 </inputs>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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46 <outputs>
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47 <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
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48 </outputs>
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49 <tests>
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50 <!-- 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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51 <test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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52 <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
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53 <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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54 <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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55 <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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56 </repeat>
1
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57 <expand macro="tests/intensity_image_diff" name="result" value="input1_times_2.tiff" ftype="tiff"/>
0
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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58 </test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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59 <!-- Unary negation operator -->
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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60 <test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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61 <param name="expression" 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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62 <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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63 <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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64 <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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65 </repeat>
1
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66 <expand macro="tests/intensity_image_diff" name="result" value="minus_input1.tiff" ftype="tiff"/>
0
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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67 </test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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68 <!-- 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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69 <test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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70 <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
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71 <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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72 <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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73 <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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74 </repeat>
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75 <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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76 <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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77 <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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78 </repeat>
1
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79 <expand macro="tests/intensity_image_diff" name="result" value="ones.tiff" ftype="tiff"/>
0
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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80 </test>
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81 <!-- Parentheses -->
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82 <test>
33b2ca53a566 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/image_math commit b356d76025941b691c156f8ff931cd759d35b107
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83 <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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84 <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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85 <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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86 <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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87 </repeat>
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88 <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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89 <param name="image" value="ones.tiff" />
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90 <param name="name" value="input2" />
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91 </repeat>
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92 <expand macro="tests/intensity_image_diff" name="result" value="half_of_input1_plus_one.tiff" ftype="tiff"/>
0
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93 </test>
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94 <!-- Abs -->
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95 <test>
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96 <param name="expression" value="abs(input)" />
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97 <repeat name="inputs">
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98 <param name="image" value="input1.tiff" />
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99 <param name="name" value="input" />
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100 </repeat>
1
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101 <expand macro="tests/intensity_image_diff" name="result" value="input1_abs.tiff" ftype="tiff"/>
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102 </test>
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103 </tests>
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104 <help>
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105
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106 **Processes images according to pixel-wise arithmetic expressions.**
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107
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108 The supported pixel-wise expressions are:
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109
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110 - Addition, subtraction, multiplication, and division (``+``, ``-``, ``*``, ``/``)
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111 - Integer division (e.g., ``input // 2``)
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112 - Power (e.g., ``input ** 2``)
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113 - Negation (e.g., ``-input``)
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114 - Absolute values (e.g., ``abs(input)``)
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115 - Square root (e.g., ``sqrt(input)``)
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116 - Combinations of the above (also using parentheses)
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117
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118 Examples:
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119
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120 - **Negate an image.**
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121 Expression: ``-image``
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122 where ``image`` is an arbitrary input image.
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123
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124 - **Mean of two images.**
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125 Expression: ``(image1 + image2) / 2``
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126 where ``image1`` and `image2` are two arbitrary input images.
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127
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128 - **Perform division avoiding division-by-zero.**
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129 Expression: ``image1 / (abs(image2) + 1e-8)``
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130 where ``image1`` and `image2` are two arbitrary input images.
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131
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132 </help>
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133 <citations>
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134 <citation type="doi">10.1038/s41586-020-2649-2</citation>
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135 </citations>
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136 </tool>