Mercurial > repos > imgteam > 3d_tensor_feature_dimension_reduction
comparison 3d_tensor_feature_dimension_reduction.xml @ 0:e8f64a98cbc6 draft default tip
"planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/3d_tensor_feature_dimension_reduction/ commit e82400162e337b36c29d6e79fb2deb9871475397"
author | imgteam |
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date | Thu, 20 Jan 2022 00:45:01 +0000 |
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1 <tool id="ip_3d_tensor_feature_dimension_reduction" name="Dimensionality Reduction" version="0.0.1" profile="20.05"> | |
2 <description>for features of 3D tensor data using UMAP</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.20.2">numpy</requirement> | |
5 <requirement type="package" version="3.6.0">h5py</requirement> | |
6 <requirement type="package" version="2020.10.1">tifffile</requirement> | |
7 <requirement type="package" version="0.5.2">umap-learn</requirement> | |
8 </requirements> | |
9 <command detect_errors="aggressive"><![CDATA[ | |
10 ln -s '$fn_in' ./input.h5 && | |
11 python '$__tool_directory__/3d_tensor_feature_dimension_reduction.py' | |
12 ./input.h5 | |
13 '$nCh' | |
14 ./output.tif | |
15 ]]> | |
16 </command> | |
17 <inputs> | |
18 <param name="fn_in" type="data" format="hdf5" label="3D tensor data (rows x cols x features)" /> | |
19 <param name="nCh" type="integer" value="5" optional="true" min="1" max="10" label="Reduced dimensions of features" /> | |
20 </inputs> | |
21 <outputs> | |
22 <data format="tiff" name="fn_out" from_work_dir="output.tif" /> | |
23 </outputs> | |
24 <tests> | |
25 <test> | |
26 <param name="fn_in" value="tensor.h5"/> | |
27 <param name="nCh" value="3"/> | |
28 <output name="fn_out" value="tensor_r.tif" ftype="tiff" compare="sim_size"/> | |
29 </test> | |
30 </tests> | |
31 <help> | |
32 **What it does** | |
33 | |
34 This tool performs dimensionality reduction for features of 3D tensor data (rows x cols x features) using UMAP. The results will be saved as a multi-channel 32-bit TIFF image (features x rows x cols). | |
35 </help> | |
36 <citations> | |
37 </citations> | |
38 </tool> |