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planemo upload for repository https://github.com/goeckslab/gleam.git commit 11356473f09dd54d86af28b74bd9ed097d07ca04
author goeckslab
date Thu, 03 Jul 2025 23:48:01 +0000
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1 <tool id="tiling_pyhist" name="Tile Images with PyHIST" version="1.0.0">
2 <description>Tile pathology images using PyHIST in parallel</description>
3
4 <requirements>
5 <container type="docker">quay.io/goeckslab/galaxy-tiler:1.0.0</container>
6 </requirements>
7 <stdio>
8 <exit_code range="137" level="fatal_oom" description="Out of Memory" />
9 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
10 </stdio>
11 <command><![CDATA[
12 python "$__tool_directory__/tiling_pyhist.py"
13 #for $i, $img in enumerate($input_collection)
14 --input '${img}' --original_name "${img.element_identifier}"
15 #end for
16 --output_zip '$output_zip'
17 ]]></command>
18
19 <inputs>
20 <param name="input_collection" type="data_collection" collection_type="list" format="svs,tiff,tif" label="Input Image Collection"
21 help="Provide a dataset collection of pathology images (.svs, .tiff, .tif)." />
22 </inputs>
23
24 <outputs>
25 <data name="output_zip" format="zip" label="Image Tiles (zip)" />
26 </outputs>
27 <tests>
28 <test>
29 <param name="input_collection">
30 <collection type="list">
31 <element name="sample1" ftype="svs" value="CMU-1-Small-Region.svs" />
32 </collection>
33 </param>
34 <output name="output_zip" file="expected_output_CMU-1-Small-Region.zip" compare="sim_size" delta="10000"/>
35 </test>
36 </tests>
37 <help><![CDATA[
38 **Tile Images with PyHIST**
39
40 This tool tiles pathology images using PyHIST in parallel using Docker. It accepts a **collection** of pathology images:
41
42 - A dataset collection of individual pathology images (e.g., `.svs`, `.tiff`, `.tif`).
43
44 Each image in the collection will be processed in a batch using PyHIST. The output is a ZIP file containing tiled image folders named after the input images.
45
46 **Inputs:**
47 - **Input Image Collection**: Provide a collection of images to tile.
48 - **Output ZIP Filename**: The resulting ZIP file of tiled patches.
49
50 **Outputs:**
51 - **Tiled Images ZIP**: A single ZIP archive with all tiled outputs.
52
53 **Note**: Requires Docker on the Galaxy server. Ensure sufficient disk and CPU resources for parallel processing.
54 ]]></help>
55 <citations>
56 <citation type="doi">10.1371/journal.pcbi.1008349</citation>
57 </citations>
58 </tool>