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annotate macros.xml @ 1:ed28a1feba82 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
author bgruening
date Mon, 26 May 2025 06:54:28 +0000
parents 5bd5f26279fd
children a88a1e78702e
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5bd5f26279fd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 25cbe535af7320192ae450fb65b74c197aaceb50
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1 <macros>
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2 <token name="@TOOL_VERSION@">1.3.0</token>
1
ed28a1feba82 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/vpt commit 1011b91cc4b13f365c51661bedb27a898b1bf817
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3 <token name="@VERSION_SUFFIX@">1</token>
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4 <token name="@PROFILE@">23.0</token>
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5 <xml name="requirements">
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6 <requirements>
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7 <container type="docker">quay.io/bgruening/vpt:1.3.0-1</container>
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8 <yield/>
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9 </requirements>
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10 </xml>
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11 <xml name="creator">
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12 <creator>
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13 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
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14 <person givenName="Amirhossein" familyName="Naghsh Nilchi" email="nilchia@informatik.uni-freiburg.de" />
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15 <person givenName="Pavan" familyName="Videm" email="videmp@informatik.uni-freiburg.de" />
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16 <person givenName="Björn" familyName="Grüning" email="gruening@informatik.uni-freiburg.de" />
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17 </creator>
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18 </xml>
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19 <token name="@CMD@"><![CDATA[
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20 mkdir -p 'input/images' 'output/' &&
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21 #for $image in $input_images:
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22 ln -s '$image' 'input/images/${image.element_identifier}.${image.ext}' &&
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23 #end for
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24 ln -s '$input_micron_to_mosaic' 'input/micron_to_mosaic_pixel_transform.csv' &&
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25 ]]></token>
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26 <token name="@COMMON_ARGS@"><![CDATA[
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27 --processes \${GALAXY_SLOTS:-10}
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28 --verbose
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29 --log-file 'output/log'
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30 ]]>
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31 </token>
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32 <xml name="common_input">
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33 <param argument="--input_images" type="data" format="tiff" multiple="true" label="MEROSCOPE tiff images"/>
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34 <param argument="--input_micron_to_mosaic" type="data" format="csv" label="Micron to mosaic mapping file"/>
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35 </xml>
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36 <xml name="normalization_param" token_label="Normalization">
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37 <param name="normalization" type="select" label="@LABEL@">
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38 <option value="default">default (min-max range normalization)</option>
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39 <option value="CLAHE">CLAHE (Contrast Limited Adaptive Histogram Equalization)</option>
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40 </param>
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41 </xml>
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42 <xml name="channel_options_basic">
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43 <yield/>
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44 <option value="Cellbound1">Cellbound1</option>
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45 <option value="Cellbound2">Cellbound2</option>
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46 <option value="Cellbound3">Cellbound3</option>
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47 </xml>
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48 <xml name="channel_options_none">
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49 <expand macro="channel_options_basic">
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50 <option value="None" selected="true">None</option>
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51 <option value="DAPI">DAPI</option>
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52 <option value="PolyT">PolyT</option>
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53 <yield/>
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54 </expand>
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55 </xml>
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56 <xml name="advanced_output">
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57 <section name="advanced_output" title="Advanced output options">
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58 <param name="log" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Output log?"/>
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59 </section>
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60 </xml>
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61 <xml name="common_output">
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62 <data name="vpt_log" format="txt" from_work_dir="output/log" label="${tool.name} on ${on_string}: VPT log">
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63 <filter>advanced_output['log']</filter>
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64 </data>
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65 </xml>
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66 <xml name="sanitize_digits">
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67 <sanitizer invalid_char="">
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68 <valid initial="string.digits">
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69 <add value=","/>
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70 <add value="."/>
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71 </valid>
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72 </sanitizer>
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73 </xml>
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74 <xml name="citations">
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75 <citations>
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76 <citation type="bibtex">@Manual{github,
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77 title = {Vizgen Post-processing Tool},
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78 author = {Vizgen},
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79 organization = {Vizgen},
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80 year = {2022},
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81 url = {https://github.com/Vizgen/vizgen-postprocessing}}
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82 </citation>
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83 </citations>
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84 </xml>
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85 </macros>