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comparison cellpose.xml @ 2:e5370bb71633 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 5846f23282167df28e6cc00e1bda31523b66b5b4
author bgruening
date Sat, 15 Mar 2025 17:23:55 +0000
parents 1857781df226
children c793edde4284
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1:1857781df226 2:e5370bb71633
1 <tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.02"> 1 <tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.02">
2 <description>with Cellpose</description> 2 <description>with Cellpose</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">3.1.0</token> 4 <token name="@TOOL_VERSION@">3.1.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 <xml name="channel"> 6 <xml name="channel">
7 <option value="0" selected="true">grayscale/None</option> 7 <option value="0" selected="true">grayscale/None</option>
8 <option value="1">red</option> 8 <option value="1">red</option>
9 <option value="2">green</option> 9 <option value="2">green</option>
10 <option value="3">blue</option> 10 <option value="3">blue</option>
17 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/> 17 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
18 </stdio> 18 </stdio>
19 <version_command>echo "@VERSION@"</version_command> 19 <version_command>echo "@VERSION@"</version_command>
20 <command detect_errors="exit_code"> 20 <command detect_errors="exit_code">
21 <![CDATA[ 21 <![CDATA[
22 export MKL_NUM_THREADS=1 &&
22 export CELLPOSE_LOCAL_MODELS_PATH='cellpose_models' && 23 export CELLPOSE_LOCAL_MODELS_PATH='cellpose_models' &&
23 mkdir -p segmentation && 24 mkdir -p segmentation &&
24 ln -s '${img_in}' ./image.${img_in.ext} && 25 ln -s '${img_in}' ./image.${img_in.ext} &&
25 26
26 python '$__tool_directory__/cp_segmentation.py' 27 python '$__tool_directory__/cp_segmentation.py'
32 </command> 33 </command>
33 <configfiles> 34 <configfiles>
34 <inputs name="inputs" /> 35 <inputs name="inputs" />
35 </configfiles> 36 </configfiles>
36 <inputs> 37 <inputs>
37 <param name="img_in" type="data" format="ome.tiff,tiff,jpeg,png" label="Choose the image file for segmention (usually after registration)"/> 38 <param name="img_in" type="data" format="ome.tiff,tiff,jpg,png" label="Choose the image file for segmention (usually after registration)"/>
38 <param name="model_type" type="select" label="Choose the pre-trained model type"> 39 <param name="model_type" type="select" label="Choose the pre-trained model type">
39 <option value="nuclei" selected="true">nuclei</option> 40 <option value="nuclei" selected="true">nuclei</option>
40 <option value="cyto">cyto</option> 41 <option value="cyto">cyto</option>
41 <option value="cyto2">cyto2</option> 42 <option value="cyto2">cyto2</option>
42 <option value="cyto3">cyto3</option> 43 <option value="cyto3">cyto3</option>
113 <test expect_num_outputs="2"> 114 <test expect_num_outputs="2">
114 <param name="img_in" value="img02.png"/> 115 <param name="img_in" value="img02.png"/>
115 <param name="model_type" value="cyto"/> 116 <param name="model_type" value="cyto"/>
116 <param name="chan" value="2"/> 117 <param name="chan" value="2"/>
117 <param name="chan2" value="3"/> 118 <param name="chan2" value="3"/>
118 <param name="diameter" value="50"/> 119 <section name="options">
120 <param name="diameter" value="50"/>
121 </section>
119 <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="image_diff"/> 122 <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="image_diff"/>
120 <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="image_diff"/> 123 <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="image_diff"/>
121 </test> 124 </test>
122 <test expect_num_outputs="2"> 125 <test expect_num_outputs="2">
123 <param name="img_in" value="img02.png"/> 126 <param name="img_in" value="img02.png"/>