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comparison cellpose.xml @ 4:32153c43126c draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/cellpose commit 81c6be8cc2502367ae52bf093b838e9764b22c00
author bgruening
date Tue, 11 Feb 2025 14:48:08 +0000
parents 9186100e75b5
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3:9186100e75b5 4:32153c43126c
1 <tool id="cellpose" name="Run generalist cell and nucleus segmentation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> 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@">3.0.10</token> 4 <token name="@TOOL_VERSION@">3.1.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</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>
11 </xml> 11 </xml>
12 </macros> 12 </macros>
13 <requirements> 13 <requirements>
14 <requirement type="package" version="@TOOL_VERSION@">cellpose</requirement> 14 <container type="docker">quay.io/biocontainers/cellpose:@TOOL_VERSION@</container>
15 </requirements> 15 </requirements>
16 <stdio> 16 <stdio>
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>
57 <param argument="flow_threshold" type="float" min="0" value="0.4" label="Flow error threshold (all cells with errors below threshold are kept) (not used for 3D)"/> 57 <param argument="flow_threshold" type="float" min="0" value="0.4" label="Flow error threshold (all cells with errors below threshold are kept) (not used for 3D)"/>
58 <param argument="cellprob_threshold" type="float" value="0.0" label="Cell probability threshold (all pixels with prob above threshold kept for masks)"/> 58 <param argument="cellprob_threshold" type="float" value="0.0" label="Cell probability threshold (all pixels with prob above threshold kept for masks)"/>
59 <param argument="niter" type="integer" min="0" value="0" label="Number of iterations" 59 <param argument="niter" type="integer" min="0" value="0" label="Number of iterations"
60 help="By defalut, sets the number of iterations to be proportional to the ROI diameter. For longer ROIs, more iterations might be needed."/> 60 help="By defalut, sets the number of iterations to be proportional to the ROI diameter. For longer ROIs, more iterations might be needed."/>
61 <param argument="do_3D" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to run 3D segmentation on 4D image input?"/> 61 <param argument="do_3D" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to run 3D segmentation on 4D image input?"/>
62 <param argument="tile" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Tiles image for test time augmentation and to ensure GPU memory usage limited (recommended)"/>
63 <param argument="rescale" type="float" value="" optional="true" label="If diameter is set to None, and rescale is not None, then rescale is used instead of diameter for resizing image"/> 62 <param argument="rescale" type="float" value="" optional="true" label="If diameter is set to None, and rescale is not None, then rescale is used instead of diameter for resizing image"/>
64 <param argument="invert" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to invert image pixel intensity before running network?"/> 63 <param argument="invert" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to invert image pixel intensity before running network?"/>
65 </section> 64 </section>
66 </inputs> 65 </inputs>
67 <outputs> 66 <outputs>
74 <test expect_num_outputs="2"> 73 <test expect_num_outputs="2">
75 <param name="img_in" value="img02.png"/> 74 <param name="img_in" value="img02.png"/>
76 <param name="model_type" value="cyto"/> 75 <param name="model_type" value="cyto"/>
77 <param name="chan" value="2"/> 76 <param name="chan" value="2"/>
78 <param name="chan2" value="3"/> 77 <param name="chan2" value="3"/>
79 <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="sim_size" delta_frac="0.1"/> 78 <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="image_diff"/>
80 <output name="cp_segm" file="img02_cp_segm_cyto.png" compare="sim_size" delta_frac="0.1"/> 79 <output name="cp_segm" file="img02_cp_segm_cyto.png" compare="image_diff"/>
81 </test> 80 </test>
82 <test expect_num_outputs="2"> 81 <test expect_num_outputs="2">
83 <param name="img_in" value="img02.png"/> 82 <param name="img_in" value="img02.png"/>
84 <param name="model_type" value="cyto2"/> 83 <param name="model_type" value="cyto2"/>
85 <param name="chan" value="2"/> 84 <param name="chan" value="2"/>
86 <param name="chan2" value="3"/> 85 <param name="chan2" value="3"/>
87 <output name="cp_mask" file="img02_cp_masks_cyto2.tif" compare="sim_size" delta_frac="0.1"/> 86 <output name="cp_mask" file="img02_cp_masks_cyto2.tif" compare="image_diff"/>
88 <output name="cp_segm" file="img02_cp_segm_cyto2.png" compare="sim_size" delta_frac="0.1"/> 87 <output name="cp_segm" file="img02_cp_segm_cyto2.png" compare="image_diff"/>
89 </test> 88 </test>
90 <test expect_num_outputs="2"> 89 <test expect_num_outputs="2">
91 <param name="img_in" value="img02.png"/> 90 <param name="img_in" value="img02.png"/>
92 <param name="model_type" value="cyto3"/> 91 <param name="model_type" value="cyto3"/>
93 <param name="chan" value="2"/> 92 <param name="chan" value="2"/>
94 <param name="chan2" value="3"/> 93 <param name="chan2" value="3"/>
95 <output name="cp_mask" file="img02_cp_masks_cyto3.tif" compare="sim_size" delta_frac="0.1"/> 94 <output name="cp_mask" file="img02_cp_masks_cyto3.tif" compare="image_diff"/>
96 <output name="cp_segm" file="img02_cp_segm_cyto3.png" compare="sim_size" delta_frac="0.1"/> 95 <output name="cp_segm" file="img02_cp_segm_cyto3.png" compare="image_diff"/>
97 </test> 96 </test>
98 <test expect_num_outputs="2"> 97 <test expect_num_outputs="2">
99 <param name="img_in" value="img02.png"/> 98 <param name="img_in" value="img02.png"/>
100 <param name="model_type" value="nuclei"/> 99 <param name="model_type" value="nuclei"/>
101 <param name="chan" value="2"/> 100 <param name="chan" value="2"/>
102 <param name="chan2" value="3"/> 101 <param name="chan2" value="3"/>
103 <output name="cp_mask" file="img02_cp_masks_nuclei.tif" compare="sim_size" delta_frac="0.1"/> 102 <output name="cp_mask" file="img02_cp_masks_nuclei.tif" compare="image_diff"/>
104 <output name="cp_segm" file="img02_cp_segm_nuclei.png" compare="sim_size" delta_frac="0.1"/> 103 <output name="cp_segm" file="img02_cp_segm_nuclei.png" compare="image_diff"/>
105 </test> 104 </test>
106 <test expect_num_outputs="2"> 105 <test expect_num_outputs="2">
107 <param name="img_in" value="img02.png"/> 106 <param name="img_in" value="img02.png"/>
108 <param name="model_type" value="cyto"/> 107 <param name="model_type" value="cyto"/>
109 <param name="chan" value="2"/> 108 <param name="chan" value="2"/>
110 <param name="chan2" value="1"/> 109 <param name="chan2" value="1"/>
111 <output name="cp_mask" file="img02_cp_masks_chan.tif" compare="sim_size" delta_frac="0.1"/> 110 <output name="cp_mask" file="img02_cp_masks_chan.tif" compare="image_diff"/>
112 <output name="cp_segm" file="img02_cp_segm_chan.png" compare="sim_size" delta_frac="0.1"/> 111 <output name="cp_segm" file="img02_cp_segm_chan.png" compare="image_diff"/>
113 </test> 112 </test>
114 <test expect_num_outputs="2"> 113 <test expect_num_outputs="2">
115 <param name="img_in" value="img02.png"/> 114 <param name="img_in" value="img02.png"/>
116 <param name="model_type" value="cyto"/> 115 <param name="model_type" value="cyto"/>
117 <param name="chan" value="2"/> 116 <param name="chan" value="2"/>
118 <param name="chan2" value="3"/> 117 <param name="chan2" value="3"/>
119 <param name="diameter" value="50"/> 118 <param name="diameter" value="50"/>
120 <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="sim_size" delta_frac="0.1"/> 119 <output name="cp_mask" file="img02_cp_masks_diameter.tif" compare="image_diff"/>
121 <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="sim_size" delta_frac="0.1"/> 120 <output name="cp_segm" file="img02_cp_segm_diameter.png" compare="image_diff"/>
122 </test> 121 </test>
123 <test expect_num_outputs="2"> 122 <test expect_num_outputs="2">
124 <param name="img_in" value="img02.png"/> 123 <param name="img_in" value="img02.png"/>
125 <param name="use_gpu" value="true"/> 124 <param name="use_gpu" value="true"/>
126 <param name="model_type" value="cyto"/> 125 <param name="model_type" value="cyto"/>
127 <param name="chan" value="2"/> 126 <param name="chan" value="2"/>
128 <param name="chan2" value="3"/> 127 <param name="chan2" value="3"/>
129 <output name="cp_mask" file="img02_cp_masks_gpu.tif" compare="sim_size" delta_frac="0.1"/> 128 <output name="cp_mask" file="img02_cp_masks_gpu.tif" compare="image_diff"/>
130 <output name="cp_segm" file="img02_cp_segm_gpu.png" compare="sim_size" delta_frac="0.1"/> 129 <output name="cp_segm" file="img02_cp_segm_gpu.png" compare="image_diff"/>
131 </test> 130 </test>
132 <test expect_num_outputs="1"> 131 <test expect_num_outputs="1">
133 <param name="img_in" value="img02.png"/> 132 <param name="img_in" value="img02.png"/>
134 <param name="model_type" value="cyto"/> 133 <param name="model_type" value="cyto"/>
135 <param name="chan" value="2"/> 134 <param name="chan" value="2"/>
136 <param name="chan2" value="3"/> 135 <param name="chan2" value="3"/>
137 <param name="show_segmentation" value="false"/> 136 <param name="show_segmentation" value="false"/>
138 <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="sim_size" delta_frac="0.1"/> 137 <output name="cp_mask" file="img02_cp_masks_cyto.tif" compare="image_diff"/>
139 </test> 138 </test>
140 </tests> 139 </tests>
141 <help> 140 <help>
142 <![CDATA[ 141 <![CDATA[
143 Cellpose: A generalist algorithm for cell and nucleus segmentation. 142 Cellpose: A generalist algorithm for cell and nucleus segmentation.