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1 <tool id="netisce8" name="Netisce Step 8" version="0.1.0" python_template_version="3.5.0">
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2 <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>
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3
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4 <requirements>
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5 <requirement type="package" version="1.1.5">pandas</requirement>
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6 <requirement type="package" version="1.7.3">scipy</requirement>
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7 <requirement type="package" version="3.0.1">matplotlib</requirement>
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8 <requirement type="package" version="3.0.1">matplotlib.pyplot</requirement>
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9 <requirement type="package" version="1.0.1">sklearn.decomposition</requirement>
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10 <requirement type="package" version="1.19.5">numpy</requirement>
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11 <requirement type="package" version="1.0.1">sklearn.datasets</requirement>
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12 <requirement type="package" version="1.0.1">sklearn.cluster</requirement>
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13 <requirement type="package" version="1.3.0">yellowbrick.cluster.elbow</requirement>
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14 <requirement type="package" version="3.5.0">sys</requirement>
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15 <requirement type="package" version="3.5.0">os</requirement>
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16 </requirements>
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17
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18 <command> python3 '$__tool_directory__/bin/kmeans_full.py' '$experimental_attractors','$random_attractors'</command>
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19
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20 <inputs>
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21 <param name="experimental_attractors" type="data" format="tabular" label="Attractors Generated from Experimental Samples"/>
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22 <param name="random_attractors" type="data" format="tabular" label="Attractors Generated from randomly generated initial states."/>
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23 </inputs>
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24
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25 <outputs>
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26 <data name="output1" format="png" from_work_dir="elbow.png" label="Elbow Metric Plot"/>
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27 <data name="output2" format="png" from_work_dir="silhouette.png" label="Silhouette Metric Plot"/>
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28 <data name="output3" format="txt" from_work_dir="kmeans.txt" label="K-means clustering of attractors"/>
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29 </outputs>
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30
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31 <tests>
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32 <test>
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33 <param name="datasets" value="attrs_exp.tsv,attrs_insilico.tsv"/>
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34 <output name="output1" value="elbow.png" ftype="png" />
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35 <output name="output2" value="silhouette.png" ftype="png" />
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36 <output name="output3" value="kmeans.txt" ftype="txt" />
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37 </test>
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38 </tests>
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39
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40 <help>
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41 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.
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42 Required Inputs:
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43 1. Experimental Attractors of all samples of interest, Insilico Attractors of all samples of interest
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44 </help>
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45
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46 </tool> |