Mercurial > repos > galaxyp > qupath_roi_splitter

annotate qupath_roi_splitter.xml @ 4:0ce973d5935f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 80eecd9912892296aad3231be75fcee3cc6a6b02
author galaxyp
date Mon, 02 Sep 2024 19:07:15 +0000
parents 180b6dc5735a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
1 <tool id="qupath_roi_splitter" name="QuPath ROI Splitter" version="@VERSION@+galaxy@VERSION_SUFFIX@">
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
2 <description>Split ROI coordinates of QuPath TMA annotation by cell type (classification)</description>
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
3 <macros>
4
0ce973d5935f planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 80eecd9912892296aad3231be75fcee3cc6a6b02
galaxyp
parents: 3
diff changeset
4 <token name="@VERSION@">0.3.2</token>
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
6 </macros>
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
7 <requirements>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
8 <requirement type="package" version="3.0.1">geojson</requirement>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
9 <requirement type="package" version="1.24.2">numpy</requirement>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
10 <requirement type="package" version="4.7.0">opencv</requirement>
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
11 <requirement type="package" version="2.0.0">pandas</requirement>
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
12 </requirements>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
13 <command detect_errors="exit_code"><![CDATA[
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
14 #for $input in $input_collection
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
15 python3 '$__tool_directory__/qupath_roi_splitter.py'
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
16 --qupath_roi '$input'
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
17 $optional.fill
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
18 $optional.all
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
19 $optional.img
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
20 &&
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
21 #end for
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
22 mkdir out
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
23 && mv *.txt out/
3
180b6dc5735a planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6
galaxyp
parents: 2
diff changeset
24 #if $optional.img
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
25 && mv *.png out/
3
180b6dc5735a planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6
galaxyp
parents: 2
diff changeset
26 #end if
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
27 ]]></command>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
28 <inputs>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
29 <param name="input_collection" type="data_collection" format="geojson" label="Input QuPath annotation" help="Collection containing GeoJSON files"/>
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
30 <section name="optional" title="Optional">
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
31 <param name="fill" type="boolean" truevalue="--fill" falsevalue="" checked="false" label="Fill ROIs" help="Fill pixels in ROIs"/>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
32 <param name="all" type="boolean" truevalue="--all" falsevalue="" checked="false" label="Extract all" help="Extracts all ROIs"/>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
33 <param name="img" type="boolean" truevalue="--img" falsevalue="" checked="false" label="Generate image" help="Generates image from ROIs"/>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
34 </section>
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
35 </inputs>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
36 <outputs>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
37 <collection name="output_txts" type="list" label="${tool.name} on ${on_string}: ROI data">
3
180b6dc5735a planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6
galaxyp
parents: 2
diff changeset
38 <discover_datasets pattern="(?P&lt;name&gt;.*\.txt)" directory="out" visible="false" ext="tabular"/>
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
39 </collection>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
40 <collection name="output_imgs" type="list" label="${tool.name} on ${on_string}: Images of ROIs">
3
180b6dc5735a planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6
galaxyp
parents: 2
diff changeset
41 <filter>optional['img']</filter>
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
42 <discover_datasets pattern="(?P&lt;name&gt;.*\.png)" directory="out" visible="false" ext="png"/>
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
43 </collection>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
44 </outputs>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
45 <tests>
3
180b6dc5735a planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit e3d24f3dc7a9812f8fa4447c9391e5bd3b5d4dc6
galaxyp
parents: 2
diff changeset
46 <test expect_num_outputs="2">
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
47 <param name="input_collection">
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
48 <collection type="list">
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
49 <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
galaxyp
parents:
diff changeset
50 <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
galaxyp
parents:
diff changeset
51 </collection>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
52 </param>
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
53 <section name="optional">
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
54 <param name="fill" value="true"/>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
55 <param name="img" value="true"/>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
56 </section>
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
57 <output_collection name="output_txts" type="list" count="4">
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
58 <element name="F-5_Stroma.txt">
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
59 <assert_contents>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
60 <has_text text="x"/>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
61 <has_text text="y"/>
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
62 <has_text text="21153"/>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
63 <has_text text="15570"/>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
64 </assert_contents>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
65 </element>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
66 </output_collection>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
67 <output_collection name="output_imgs" type="list" count="4">
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
68 <element name="E-5_Tumor.png">
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
69 <assert_contents>
4
0ce973d5935f planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 80eecd9912892296aad3231be75fcee3cc6a6b02
galaxyp
parents: 3
diff changeset
70 <has_size value="1309478"/>
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
71 </assert_contents>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
72 </element>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
73 </output_collection>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
74 </test>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
75 </tests>
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
76 <help><![CDATA[
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
77 **QuPath ROI Splitter**
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
78
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
79 This tool extracts ROI coordinates of QuPath TMA annotation by cell type.
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
80
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
81 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
galaxyp
parents:
diff changeset
82
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
83 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
galaxyp
parents:
diff changeset
84
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
85 https://github.com/npinter/ROIsplitter
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
86 ]]></help>
2
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
87 <citations>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
88 <citation type="bibtex">
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
89 @misc{
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
90 toolsGalaxyP,
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
91 author = {Pinter, N, Föll, MC },
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
92 title = {Galaxy Proteomics Tools},
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
93 publisher = {GitHub}, journal = {GitHub repository},
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
94 year = {2024},
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
95 url = {https://github.com/galaxyproteomics/tools-galaxyp}
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
96 }
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
97 </citation>
3282b4920a34 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit 918ae25f84e7042ed36461219ff068633c1c2427
galaxyp
parents: 1
diff changeset
98 </citations>
0
bd60d4542fd4 planemo upload for repository hhttps://github.com/npinter/ROIsplitter commit cdf3e9652b10c7a0b179202129a797e32fd95909
galaxyp
parents:
diff changeset
99 </tool>