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1 <tool id="ctb_mds_plot" name="MDS Scatter Plot" version="0.1">
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2 <description>of molecule similarity</description>
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3 <requirements>
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4 <requirement type="package" version="0.13.1">scikit_learn</requirement>
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5 <requirement type="package" version="1.2.1">matplotlib</requirement>
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6 </requirements>
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7 <command interpreter='python'>
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8 mds_plot.py
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9 -i $infile
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10 --oformat $oformat
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11 -o $outfile
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12 </command>
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13 <inputs>
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14 <param name="infile" type="data" format="binary" label="Similarity Matrix"/>
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15 <param name='oformat' type='select' format='text' label="Format of the resulting picture">
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16 <option value='png'>PNG</option>
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17 <option value='svg'>SVG</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data type="data" format="png" name="outfile" label="${tool.name} on ${on_string}"></data>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="infile" ftype="tabular" value="sm.dat" />
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26 <output ftype="png" name="outfile" file='mds_plot_on_sm_dat.png' />
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27 </test>
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28 </tests>
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29 <help>
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30
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31 **Note**. You need an NxN similarity matrix as input. Use the NxN Clustering tool to generate one.
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32
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33 **What it does**
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34
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35 Scatter plot of similarity matrix after embeding in 2D coordinates using Multidimensional Scaling (MDS).
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36
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37 -----
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38
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39 **Example**
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40
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41 * input::
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42 Similarity Matrix
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43
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44 * output::
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45
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46 Scatter plot
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47
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48 .. image:: $PATH_TO_IMAGES/mds_plot.png
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49
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50 </help>
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51
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52 </tool>
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