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annotate scale_image.xml @ 4:3179853faae9 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:26:23 +0000
parents d09507d3fb0e
children 85666e555698
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3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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1 <tool id="ip_scale_image" name="Scale image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>with scikit-image</description>
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imgteam
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3 <macros>
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4 <import>creators.xml</import>
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5 <import>tests.xml</import>
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6 <token name="@TOOL_VERSION@">0.18.3</token>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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7 <token name="@VERSION_SUFFIX@">0</token>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
imgteam
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8 </macros>
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9 <creator>
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10 <expand macro="creators/bmcv" />
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11 </creator>
3
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12 <edam_operations>
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13 <edam_operation>operation_3443</edam_operation>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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14 </edam_operations>
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15 <xrefs>
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16 <xref type="bio.tools">scikit-image</xref>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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17 <xref type="biii">scikit-image</xref>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
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18 </xrefs>
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19 <requirements>
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20 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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21 <requirement type="package" version="10.0.1">pillow</requirement>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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22 <requirement type="package" version="1.24.4">numpy</requirement>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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23 <requirement type="package" version="2021.7.2">tifffile</requirement>
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24 </requirements>
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25 <command detect_errors="aggressive"><![CDATA[
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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27 python '$__tool_directory__/scale_image.py' '$input'
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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29 ./output.${input.ext}
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30
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31 --scale '$scale'
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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32 --order $order
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33 $antialias
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34
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35 && mv ./output.${input.ext} ./output
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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36
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37 ]]></command>
0
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 <inputs>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 <param name="input" type="data" format="png" label="Image file"/>
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40 <param argument="--scale" type="text" value="1" label="Scaling factor" help="Use either a single scaling factor (uniform scaling), or a comma-separated list of scaling factors (anistropic scaling). For a 2-D single-channel or RGB image, the first scaling factor corresponds to the image width and the second corresponds to the image height. For images with 3 or more axes, the last axis is assumed to correspond to the image channels if uniform scaling is used (a single value)."/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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41 <param argument="--order" type="select" label="Interpolation method">
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42 <option value="0">Nearest-neighbor</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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43 <option value="1" selected="true">Bi-linear</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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44 <option value="2">Bi-cubic</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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45 </param>
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46 <param name="antialias" type="boolean" truevalue="--antialias" falsevalue="" checked="true" label="Enable anti-aliasing" help="This should only be used for down-scaling."/>
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47 </inputs>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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48 <outputs>
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49 <data name="output" from_work_dir="output" format_source="input" metadata_source="input"/>
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50 </outputs>
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51 <tests>
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52 <!-- Test PNG, without antialias -->
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53 <test>
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54 <param name="input" value="input1_binary_rgb.png"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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55 <param name="scale" value="0.5"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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56 <param name="antialias" value="false"/>
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57 <param name="order" value="0"/>
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58 <expand macro="tests/binary_image_diff" name="output" value="uniform_binary.png" ftype="png"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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59 </test>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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60 <!-- Test PNG, uniform scaling -->
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61 <test>
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62 <param name="input" value="input1_binary_rgb.png"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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63 <param name="scale" value="0.5"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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64 <expand macro="tests/intensity_image_diff" name="output" value="uniform.png" ftype="png"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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65 </test>
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66 <!-- Test PNG, anistropic scaling -->
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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67 <test>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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68 <param name="input" value="input1_binary_rgb.png"/>
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69 <param name="scale" value="0.5, 0.8"/>
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70 <expand macro="tests/intensity_image_diff" name="output" value="anisotropic.png" ftype="png"/>
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71 </test>
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72 <test>
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73 <param name="input" value="input1_binary_rgb.png"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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74 <param name="scale" value="0.5, 0.8, 1"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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75 <expand macro="tests/intensity_image_diff" name="output" value="anisotropic.png" ftype="png"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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76 </test>
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77 <!-- Test TIFF, normalized -->
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78 <test>
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79 <param name="input" value="input2_normalized.tiff"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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80 <param name="scale" value="0.5"/>
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81 <expand macro="tests/intensity_image_diff" name="output" value="normalized.tiff" ftype="tiff"/>
3179853faae9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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82 </test>
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83 <!-- Test TIFF, not normalized -->
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84 <test>
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85 <param name="input" value="input3_not_normalized.tiff"/>
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86 <param name="scale" value="0.5"/>
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87 <expand macro="tests/intensity_image_diff" name="output" value="not_normalized.tiff" ftype="tiff"/>
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88 </test>
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89 </tests>
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90 <help>
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91
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92 **Scales an image using one or more scaling factors.**
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93
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94 The image is rescaled uniformly along all axes, or anistropically if multiple scale factors are given.
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95
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96 This operation preserves both the brightness of the image, and the range of values.
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97
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98 </help>
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99 <citations>
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100 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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101 </citations>
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102 </tool>