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