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comparison chemfp_clustering/nxn_clustering.xml @ 0:354d3c6bb894 draft

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author bgruening
date Thu, 15 Aug 2013 03:27:06 -0400
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1 <tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.2">
2 <description>of molecular fingerprints</description>
3 <requirements>
4 <requirement type="package" version="1.7.0">numpy</requirement>
5 <requirement type="package" version="1.1p1">chemfp</requirement>
6 <requirement type="package" version="1.2.1">matplotlib</requirement>
7 <requirement type="package" version="0.12.0">scipy</requirement>
8 <requirement type="package" version="2.3.2">openbabel</requirement>
9 </requirements>
10 <command interpreter='python'>
11 nxn_clustering.py
12 -i $infile
13 -t $threshold
14 #if str($output_files) in ['both', 'image']:
15 --cluster $image
16 #end if
17 #if str($output_files) in ['both', 'matrix']:
18 --smatrix $smilarity_matrix
19 #end if
20 --oformat $oformat
21 </command>
22 <inputs>
23 <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/>
24 <param name='threshold' type='float' value='0.0' />
25 <param name='oformat' type='select' format='text' label="Format of the resulting picture">
26 <option value='png'>PNG</option>
27 <option value='svg'>SVG</option>
28 </param>
29 <param name='output_files' type='select' format='text' label="Output options">
30 <option value='both'>NxN matrix and Image</option>
31 <option value='image'>Image</option>
32 <option value='matrix'>NxN Matrix</option>
33 </param>
34
35 </inputs>
36 <outputs>
37 <data name="image" type="data" format="svg" label="${tool.name} on ${on_string} - Cluster Image">
38 <filter>output_files == "both" or output_files == "image"</filter>
39 <change_format>
40 <when input="oformat" value="png" format="png"/>
41 </change_format>
42 </data>
43 <data name="smilarity_matrix" format="binary" label="${tool.name} on ${on_string} - Similarity Matrix">
44 <filter>output_files == "both" or output_files == "matrix"</filter>
45 </data>
46 </outputs>
47 <tests>
48 <test>
49 <param name="infile" ftype="fps" value="q.fps" />
50 <param name='treshold' value='0.75' />
51 <param name='output_files' value='image' />
52 <output ftype="svg" name="outfile" file='NxN_Clustering_on_q.svg' />
53 </test>
54 </tests>
55 <help>
56
57 .. class:: infomark
58
59 **What this tool does**
60
61 Generating hierarchical clusters and visualizing clusters with dendrograms.
62 For the clustering and the fingerprint handling the chemfp_ project is used.
63
64 .. _chemfp: http://chemfp.com/
65
66 -----
67
68 .. class:: warningmark
69
70 **Hint**
71
72 The plotting of the cluster image is sensible only with a small dataset.
73
74 -----
75
76 .. class:: infomark
77
78 **Input**
79
80 Molecular fingerprints in FPS format. Open Babel Fastsearch index is not supported.
81
82 * Example::
83
84 - fingerprints in FPS format
85
86 #FPS1
87 #num_bits=881
88 #type=CACTVS-E_SCREEN/1.0 extended=2
89 #software=CACTVS/unknown
90 #source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat
91 #date=2012-02-09T13:20:37
92 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e
93 19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000 55169009
94 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e
95 19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000 55079807
96 ........
97
98 - Tanimoto threshold : 0.8 (between 0 and 1)
99
100 -----
101
102 .. class:: informark
103
104 **Output**
105
106 * Example::
107
108 .. image:: $PATH_TO_IMAGES/NxN_clustering.png
109
110 -----
111
112 .. class:: infomark
113
114 **Cite**
115
116 The chemfp_ project from Andrew Dalke!
117
118 .. _chemfp: http://chemfp.com/
119
120 </help>
121
122 </tool>