Mercurial > repos > galaxyp > qupath_roi_splitter

annotate qupath_roi_splitter.xml @ 0:bd60d4542fd4 draft

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planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
author galaxyp
date Tue, 25 Apr 2023 09:29:53 +0000
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children f955895aed01
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bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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1 <tool id="qupath_roi_splitter" name="QuPath ROI Splitter" version="0.1.0">
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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2 <description>Split ROI coordinates of QuPath TMA annotation by cell type (classification)</description>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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3 <requirements>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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4 <requirement type="package" version="3.0.1">geojson</requirement>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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5 <requirement type="package" version="1.24.2">numpy</requirement>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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6 <requirement type="package" version="4.7.0">opencv</requirement>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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7 <requirement type="package" version="2.0.0">pandas</requirement>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
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8 </requirements>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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9 <command detect_errors="exit_code"><![CDATA[
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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10 #for $input in $input_collection
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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11 python3 '$__tool_directory__/qupath_roi_splitter.py' --qupath_roi '$input' &&
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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12 #end for
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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13 mkdir out &&
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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14 mv *.txt out/
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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15 ]]></command>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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16 <inputs>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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17 <param name="input_collection" type="data_collection" format="geojson" label="Input QuPath annotation" help="Collection containing GeoJSON files"/>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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18 </inputs>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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19 <outputs>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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20 <collection name="output_txts" type="list" label="${tool.name} on ${on_string}: ROI data">
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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21 <discover_datasets pattern="__name_and_ext__" directory="out" visible="false" format="txt"/>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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22 </collection>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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23 </outputs>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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24 <tests>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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25 <test>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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26 <param name="input_collection">
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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27 <collection type="list">
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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28 <element name="annotations_TMA_E-5.geojson" value="annotations_TMA_E-5.geojson" />
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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29 <element name="annotations_TMA_F-5.geojson" value="annotations_TMA_F-5.geojson" />
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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30 </collection>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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31 </param>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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32 <output_collection name="output_txts" type="list" count="4">
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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33 <element name="F-5_Stroma">
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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34 <assert_contents>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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35 <has_text text="x"/>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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36 <has_text text="y"/>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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37 <has_text text="14240"/>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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38 <has_text text="21008"/>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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39 </assert_contents>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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40 </element>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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41 </output_collection>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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42 </test>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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43 </tests>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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44 <help><![CDATA[
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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45 **QuPath ROI Splitter**
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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46
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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47 This tool extracts ROI coordinates of QuPath TMA annotation by cell type.
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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48
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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49 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.
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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50
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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51 Output: A list of text files containing the ROI coordinates for each cell type.
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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52
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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53 https://github.com/npinter/ROIsplitter
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
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54 ]]></help>
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55 </tool>