Mercurial > repos > laurenmarazzi > netisce_test
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/myTools/8_kmeans.xml Wed Dec 22 16:00:34 2021 +0000 @@ -0,0 +1,46 @@ +<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> \ No newline at end of file