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view tools/myTools/8_kmeans.xml @ 1:7e5c71b2e71f draft default tip
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author | laurenmarazzi |
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date | Wed, 22 Dec 2021 16:00:34 +0000 |
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<tool id="netisce8" name="Netisce Step 8" version="0.1.0" python_template_version="3.5.0"> <description>This tool computes the optimal k value using Elbow and Silhouette Metric and clusters the attractors generated from experimental data and random initial states to the k clusters </description> <requirements> <requirement type="package" version="1.1.5">pandas</requirement> <requirement type="package" version="1.7.3">scipy</requirement> <requirement type="package" version="3.0.1">matplotlib</requirement> <requirement type="package" version="3.0.1">matplotlib.pyplot</requirement> <requirement type="package" version="1.0.1">sklearn.decomposition</requirement> <requirement type="package" version="1.19.5">numpy</requirement> <requirement type="package" version="1.0.1">sklearn.datasets</requirement> <requirement type="package" version="1.0.1">sklearn.cluster</requirement> <requirement type="package" version="1.3.0">yellowbrick.cluster.elbow</requirement> <requirement type="package" version="3.5.0">sys</requirement> <requirement type="package" version="3.5.0">os</requirement> </requirements> <command> python3 '$__tool_directory__/bin/kmeans_full.py' '$experimental_attractors','$random_attractors'</command> <inputs> <param name="experimental_attractors" type="data" format="tabular" label="Attractors Generated from Experimental Samples"/> <param name="random_attractors" type="data" format="tabular" label="Attractors Generated from randomly generated initial states."/> </inputs> <outputs> <data name="output1" format="png" from_work_dir="elbow.png" label="Elbow Metric Plot"/> <data name="output2" format="png" from_work_dir="silhouette.png" label="Silhouette Metric Plot"/> <data name="output3" format="txt" from_work_dir="kmeans.txt" label="K-means clustering of attractors"/> </outputs> <tests> <test> <param name="datasets" value="attrs_exp.tsv,attrs_insilico.tsv"/> <output name="output1" value="elbow.png" ftype="png" /> <output name="output2" value="silhouette.png" ftype="png" /> <output name="output3" value="kmeans.txt" ftype="txt" /> </test> </tests> <help> This tool computes the optimal k value using Elbow and Silhouette Metric and clusters the attractors generated from experimental data and random initial states to the k clusters. Required Inputs: 1. Experimental Attractors of all samples of interest, Insilico Attractors of all samples of interest </help> </tool>