Mercurial > repos > bgruening > chemfp
comparison sdf2fps.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 |
parents | |
children | 0d88631bb7de |
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1:43a9e7d9b24f | 2:70b071de9bee |
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1 <tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="0.2"> | |
2 <description>extract fingerprints from sdf files metadata</description> | |
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism--> | |
4 <requirements> | |
5 <requirement type="package" version="1.1p1">chemfp</requirement> | |
6 <requirement type="package" version="2.4.1">openbabel</requirement> | |
7 </requirements> | |
8 <command> | |
9 <![CDATA[ | |
10 sdf2fps --pubchem '${infile}' > '${outfile}' | |
11 ]]> | |
12 </command> | |
13 <inputs> | |
14 <param name="infile" type='data' format="sdf" label="SDF file with fingerprints as metadata"/> | |
15 </inputs> | |
16 <outputs> | |
17 <data name="outfile" format="fps"/> | |
18 </outputs> | |
19 <tests> | |
20 <test> | |
21 <param name="infile" ftype="sdf" value="CID_2244.sdf" /> | |
22 <output name="outfile" file='sdf2fps_result1.fps' ftype="fps" lines_diff="4" /> | |
23 </test> | |
24 </tests> | |
25 <help> | |
26 <![CDATA[ | |
27 | |
28 .. class:: infomark | |
29 | |
30 **What this tool does** | |
31 | |
32 Read an input SD file, extract the fingerprints and store them in a FPS-file. | |
33 | |
34 ----- | |
35 | |
36 .. class:: infomark | |
37 | |
38 **Input** | |
39 | |
40 `SD-Format`_ | |
41 | |
42 .. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file | |
43 | |
44 * Example:: | |
45 | |
46 28434379 | |
47 -OEChem-02031205132D | |
48 | |
49 37 39 0 0 0 0 0 0 0999 V2000 | |
50 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
51 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
52 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
53 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
54 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
55 7.3704 0.9433 0.0000 C 0 0 0 0 | |
56 ...... | |
57 1 15 1 0 0 0 0 | |
58 1 35 1 0 0 0 0 | |
59 2 5 1 0 0 0 0 | |
60 2 11 1 0 0 0 0 | |
61 2 12 1 0 0 0 0 | |
62 3 12 2 0 0 0 0 | |
63 3 13 1 0 0 0 0 | |
64 4 18 1 0 0 0 0 | |
65 ...... | |
66 | |
67 >PUBCHEM_COMPOUND_CID< | |
68 28434379 | |
69 | |
70 > <PUBCHEM_COMPOUND_CANONICALIZED> | |
71 1 | |
72 | |
73 > <PUBCHEM_CACTVS_COMPLEXITY> | |
74 280 | |
75 | |
76 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> | |
77 2 | |
78 | |
79 > <PUBCHEM_CACTVS_HBOND_DONOR> | |
80 2 | |
81 | |
82 > <PUBCHEM_CACTVS_ROTATABLE_BOND> | |
83 2 | |
84 | |
85 > <PUBCHEM_CACTVS_SUBSKEYS> | |
86 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA== | |
87 | |
88 > | |
89 | |
90 ----- | |
91 | |
92 .. class:: infomark | |
93 | |
94 **Output** | |
95 | |
96 * Example:: | |
97 | |
98 #FPS1 | |
99 #num_bits=881 | |
100 #type=CACTVS-E_SCREEN/1.0 extended=2 | |
101 #software=CACTVS/unknown | |
102 #source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat | |
103 #date=2012-02-03T10:44:12 | |
104 07ce04000000000000000000000000000080060000000c0600 | |
105 00000000001a800f0000780008100000101487e9608c0bed32 | |
106 48000580644626204101b4844805901b041c2e19511e45039b | |
107 8b2924101609401b13e4080000000000010020000004008000 | |
108 0010000002000000000000 28434379 | |
109 | |
110 | |
111 ]]> | |
112 </help> | |
113 <citations> | |
114 <citation type="doi">10.1186/1758-2946-5-S1-P36</citation> | |
115 </citations> | |
116 </tool> |