Mercurial > repos > bgruening > chemfp
annotate chemfp_sdf2fps/sdf2fps.xml @ 1:43a9e7d9b24f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
author | bgruening |
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date | Sun, 01 Nov 2015 10:27:01 -0500 |
parents | 354d3c6bb894 |
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rev | line source |
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0 | 1 <tool id="ctb_sdf2fps" name="SDF to Fingerprint" version="0.1.1"> |
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="2.3.2">openbabel</requirement> | |
7 </requirements> | |
8 <command> | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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9 <![CDATA[ |
0 | 10 sdf2fps --pubchem "${infile}" > "${outfile}" |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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11 ]]> |
0 | 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 </tests> | |
21 <help> | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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22 <![CDATA[ |
0 | 23 |
24 .. class:: infomark | |
25 | |
26 **What this tool does** | |
27 | |
28 Read an input SD file, extract the fingerprints and store them in a FPS-file. | |
29 | |
30 ----- | |
31 | |
32 .. class:: infomark | |
33 | |
34 **Input** | |
35 | |
36 `SD-Format`_ | |
37 | |
38 .. _`SD-Format`: http://en.wikipedia.org/wiki/Chemical_table_file | |
39 | |
40 * Example:: | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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41 |
0 | 42 28434379 |
43 -OEChem-02031205132D | |
44 | |
45 37 39 0 0 0 0 0 0 0999 V2000 | |
46 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
47 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
48 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
49 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 | |
50 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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51 7.3704 0.9433 0.0000 C 0 0 0 0 |
0 | 52 ...... |
53 1 15 1 0 0 0 0 | |
54 1 35 1 0 0 0 0 | |
55 2 5 1 0 0 0 0 | |
56 2 11 1 0 0 0 0 | |
57 2 12 1 0 0 0 0 | |
58 3 12 2 0 0 0 0 | |
59 3 13 1 0 0 0 0 | |
60 4 18 1 0 0 0 0 | |
61 ...... | |
62 | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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63 >PUBCHEM_COMPOUND_CID< |
0 | 64 28434379 |
65 | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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66 > <PUBCHEM_COMPOUND_CANONICALIZED> |
0 | 67 1 |
68 | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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69 > <PUBCHEM_CACTVS_COMPLEXITY> |
0 | 70 280 |
71 | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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72 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR> |
0 | 73 2 |
74 | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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75 > <PUBCHEM_CACTVS_HBOND_DONOR> |
0 | 76 2 |
77 | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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78 > <PUBCHEM_CACTVS_ROTATABLE_BOND> |
0 | 79 2 |
80 | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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81 > <PUBCHEM_CACTVS_SUBSKEYS> |
0 | 82 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA== |
83 | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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84 > |
0 | 85 |
86 ----- | |
87 | |
88 .. class:: infomark | |
89 | |
90 **Output** | |
91 | |
92 * Example:: | |
93 | |
94 #FPS1 | |
95 #num_bits=881 | |
96 #type=CACTVS-E_SCREEN/1.0 extended=2 | |
97 #software=CACTVS/unknown | |
98 #source=/home/mohammed/galaxy-central/database/files/000/dataset_409.dat | |
99 #date=2012-02-03T10:44:12 | |
100 07ce04000000000000000000000000000080060000000c0600 | |
101 00000000001a800f0000780008100000101487e9608c0bed32 | |
102 48000580644626204101b4844805901b041c2e19511e45039b | |
103 8b2924101609401b13e4080000000000010020000004008000 | |
104 0010000002000000000000 28434379 | |
105 | |
106 ----- | |
107 | |
108 .. class:: infomark | |
109 | |
110 **Cite** | |
111 | |
112 chemfp_ project | |
113 | |
114 .. _chemfp: http://chemfp.com/ | |
115 | |
116 | |
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43a9e7d9b24f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/chemfp commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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diff
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117 ]]> |
0 | 118 </help> |
119 </tool> |