Mercurial > repos > galaxyp > qupath_roi_splitter

annotate qupath_roi_splitter.xml @ 4:9f136ebf73ac draft

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planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
author galaxyp
date Fri, 19 Jul 2024 14:33:40 +0000
parents 24ccdcfbabac
children 17c54a716a5b
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1 <tool id="qupath_roi_splitter" name="QuPath ROI Splitter" version="@VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>Split ROI coordinates of QuPath TMA annotation by cell type (classification)</description>
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3 <macros>
4
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4 <token name="@VERSION@">0.3.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
0
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7 <requirements>
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8 <requirement type="package" version="3.0.1">geojson</requirement>
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9 <requirement type="package" version="1.24.2">numpy</requirement>
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10 <requirement type="package" version="4.7.0">opencv</requirement>
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11 <requirement type="package" version="2.0.0">pandas</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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14 #for $input in $input_collection
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15 python3 '$__tool_directory__/qupath_roi_splitter.py'
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16 --qupath_roi '$input'
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17 $optional.fill
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18 $optional.all
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19 $optional.img
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20 &&
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21 #end for
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22 mkdir out
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23 && mv *.txt out/
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24 && mv *.png out/
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25 ]]></command>
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26 <inputs>
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27 <param name="input_collection" type="data_collection" format="geojson" label="Input QuPath annotation" help="Collection containing GeoJSON files"/>
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28 <section name="optional" title="Optional">
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29 <param name="fill" type="boolean" truevalue="--fill" falsevalue="" checked="false" label="Fill ROIs" help="Fill pixels in ROIs"/>
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30 <param name="all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="Extract all" help="Extracts all ROIs"/>
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31 <param name="img" type="boolean" truevalue="--img" falsevalue="" checked="false" label="Generate image" help="Generates image from ROIs"/>
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32 </section>
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33 </inputs>
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34 <outputs>
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35 <collection name="output_txts" type="list" label="${tool.name} on ${on_string}: ROI data">
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36 <discover_datasets pattern="(?P&lt;name&gt;.*\.txt)" directory="out" visible="false" ext="txt"/>
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37 </collection>
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38 <collection name="output_imgs" type="list" label="${tool.name} on ${on_string}: Images of ROIs">
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39 <discover_datasets pattern="(?P&lt;name&gt;.*\.png)" directory="out" visible="false" ext="png"/>
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40 </collection>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input_collection">
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45 <collection type="list">
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46 <element name="annotations_TMA_E-5.geojson" value="annotations_TMA_E-5.geojson" />
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47 <element name="annotations_TMA_F-5.geojson" value="annotations_TMA_F-5.geojson" />
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48 </collection>
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49 </param>
2
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50 <section name="optional">
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51 <param name="fill" value="true"/>
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52 <param name="img" value="true"/>
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53 </section>
0
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54 <output_collection name="output_txts" type="list" count="4">
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55 <element name="F-5_Stroma.txt">
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56 <assert_contents>
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57 <has_text text="x"/>
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58 <has_text text="y"/>
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59 <has_text text="21153"/>
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60 <has_text text="15570"/>
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61 </assert_contents>
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62 </element>
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63 </output_collection>
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64 <output_collection name="output_imgs" type="list" count="4">
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65 <element name="E-5_Tumor.png">
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66 <assert_contents>
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67 <has_size value="459919"/>
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68 </assert_contents>
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69 </element>
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70 </output_collection>
0
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 **QuPath ROI Splitter**
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75
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76 This tool extracts ROI coordinates of QuPath TMA annotation by cell type.
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77
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78 Input: A collection containing GeoJSON files with QuPath annotation data. You need to run the QuPath TMA annotation script first which can be found at https://github.com/npinter/ROIsplitter.
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79
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80 Output: A list of text files containing the ROI coordinates for each cell type.
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81
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82 https://github.com/npinter/ROIsplitter
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83 ]]></help>
2
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84 <citations>
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85 <citation type="bibtex">
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86 @misc{
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87 toolsGalaxyP,
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88 author = {Pinter, N, Föll, MC },
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89 title = {Galaxy Proteomics Tools},
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90 publisher = {GitHub}, journal = {GitHub repository},
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91 year = {2024},
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92 url = {https://github.com/galaxyproteomics/tools-galaxyp}
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93 }
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94 </citation>
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95 </citations>
0
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96 </tool>