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comparison mds_plot.xml @ 0:fe542273784f draft default tip

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author bgruening
date Thu, 15 Aug 2013 03:39:14 -0400
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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>