Mercurial > repos > bgruening > chemfp
comparison nxn_clustering.xml @ 2:70b071de9bee draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author | bgruening |
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date | Sat, 20 May 2017 08:31:44 -0400 |
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children | 0d88631bb7de |
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1 <tool id="ctb_chemfp_nxn_clustering" name="NxN Clustering" version="0.4"> | |
2 <description>of molecular fingerprints</description> | |
3 <requirements> | |
4 <requirement type="package" version="1.1p1">chemfp</requirement> | |
5 <requirement type="package" version="2">python</requirement> | |
6 <requirement type="package" version="2.0.2">matplotlib</requirement> | |
7 <requirement type="package" version="0.19.0">scipy</requirement> | |
8 <requirement type="package" version="2.4.1">openbabel</requirement> | |
9 </requirements> | |
10 <command detect_errors="exit_code"> | |
11 <![CDATA[ | |
12 python '$__tool_directory__/nxn_clustering.py' | |
13 -i '$infile' | |
14 -t $threshold | |
15 #if str($output_files) in ['both', 'image']: | |
16 --cluster '$image' | |
17 #end if | |
18 #if str($output_files) in ['both', 'matrix']: | |
19 --smatrix '$smilarity_matrix' | |
20 #end if | |
21 --oformat '$oformat' | |
22 ]]> | |
23 </command> | |
24 <inputs> | |
25 <param name="infile" type="data" format="fps" label="Finperprint dataset" help="Dataset missing? See TIP below"/> | |
26 <param name='threshold' type='float' value='0.0' /> | |
27 <param name='oformat' type='select' format='text' label="Format of the resulting picture"> | |
28 <option value='png'>PNG</option> | |
29 <option value='svg'>SVG</option> | |
30 </param> | |
31 <param name='output_files' type='select' format='text' label="Output options"> | |
32 <option value='both'>NxN matrix and Image</option> | |
33 <option value='image'>Image</option> | |
34 <option value='matrix'>NxN Matrix</option> | |
35 </param> | |
36 | |
37 </inputs> | |
38 <outputs> | |
39 <data name="image" format="svg" label="${tool.name} on ${on_string} - Cluster Image"> | |
40 <filter>output_files == "both" or output_files == "image"</filter> | |
41 <change_format> | |
42 <when input="oformat" value="png" format="png"/> | |
43 </change_format> | |
44 </data> | |
45 <data name="smilarity_matrix" format="binary" label="${tool.name} on ${on_string} - Similarity Matrix"> | |
46 <filter>output_files == "both" or output_files == "matrix"</filter> | |
47 </data> | |
48 </outputs> | |
49 <tests> | |
50 <test> | |
51 <param name="infile" ftype="fps" value="targets.fps" /> | |
52 <param name='treshold' value='0.75' /> | |
53 <param name='oformat' value='svg' /> | |
54 <param name='output_files' value='image' /> | |
55 <output name="image" file='NxN_Clustering_on_q.svg' ftype="svg" compare="sim_size"/> | |
56 </test> | |
57 </tests> | |
58 <help> | |
59 <![CDATA[ | |
60 | |
61 .. class:: infomark | |
62 | |
63 **What this tool does** | |
64 | |
65 Generating hierarchical clusters and visualizing clusters with dendrograms. | |
66 For the clustering and the fingerprint handling the chemfp_ project is used. | |
67 | |
68 .. _chemfp: http://chemfp.com/ | |
69 | |
70 ----- | |
71 | |
72 .. class:: warningmark | |
73 | |
74 **Hint** | |
75 | |
76 The plotting of the cluster image is sensible only with a small dataset. | |
77 | |
78 ----- | |
79 | |
80 .. class:: infomark | |
81 | |
82 **Input** | |
83 | |
84 Molecular fingerprints in FPS format. Open Babel Fastsearch index is not supported. | |
85 | |
86 * Example:: | |
87 | |
88 - fingerprints in FPS format | |
89 | |
90 #FPS1 | |
91 #num_bits=881 | |
92 #type=CACTVS-E_SCREEN/1.0 extended=2 | |
93 #software=CACTVS/unknown | |
94 #source=/home/mohammed/galaxy-central/database/files/000/dataset_423.dat | |
95 #date=2012-02-09T13:20:37 | |
96 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701487e960cc0bed3248000580644626004101b4844805901b041c2e | |
97 19511e45039b8b2926101609401b13e40800000000000100200000040080000010000002000000000000 55169009 | |
98 07ce04000000000000000000000000000080060000000c000000000000001a800f0000780008100000701087e960cc0bed3248000580644626004101b4844805901b041c2e | |
99 19111e45039b8b2926105609401313e40800000000000100200000040080000010000002000000000000 55079807 | |
100 ........ | |
101 | |
102 - Tanimoto threshold : 0.8 (between 0 and 1) | |
103 | |
104 ----- | |
105 | |
106 .. class:: informark | |
107 | |
108 **Output** | |
109 | |
110 * Example:: | |
111 | |
112 .. image:: $PATH_TO_IMAGES/NxN_clustering.png | |
113 | |
114 | |
115 ]]> | |
116 </help> | |
117 <citations> | |
118 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation> | |
119 </citations> | |
120 </tool> |