Mercurial > repos > bgruening > openbabel
comparison filter/ob_remSmall.xml @ 0:527ecd2fc500 draft
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author | bgruening |
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date | Thu, 15 Aug 2013 03:25:06 -0400 |
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children | 125da3a296ca |
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-1:000000000000 | 0:527ecd2fc500 |
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1 <tool id="ctb_remSmall" name="Remove small molecules" version="1.0"> | |
2 <description></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="2.3.2">openbabel</requirement> | |
6 </requirements> | |
7 <command> | |
8 obabel | |
9 -i"${infile.ext}" | |
10 "${infile}" | |
11 -ocopy | |
12 -O "${outfile}" | |
13 --filter "atoms > $cutoff" | |
14 -e | |
15 2>&1 | |
16 </command> | |
17 <inputs> | |
18 <param name="infile" format="sdf,mol,mol2,cml,inchi,smi" type="data" label="Molecular input file" /> | |
19 <param name="cutoff" size="3" type="integer" value="5" label="Specify the cut-off value (only molecules with more than this number of atoms will pass the filter)" /> | |
20 </inputs> | |
21 <outputs> | |
22 <data format_source="infile" name="outfile" /> | |
23 </outputs> | |
24 <tests> | |
25 <test> | |
26 <param name="infile" ftype="smi" value="3_mol.smi" /> | |
27 <param name="cutoff" value="5" /> | |
28 <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" /> | |
29 </test> | |
30 </tests> | |
31 <help> | |
32 | |
33 .. class:: infomark | |
34 | |
35 **What this tool does** | |
36 | |
37 Filters a library of compounds and removes small molecules below a predefined input number of atoms. | |
38 | |
39 ----- | |
40 | |
41 .. class:: warningmark | |
42 | |
43 **Hint** | |
44 | |
45 Some libraries may contain molecules without a 1D/3D descriptor. These molecules may provoke crashes of any other tool. It is strongly adviced to run this tool before proceeding to any further steps. | |
46 | |
47 ----- | |
48 | |
49 .. class:: infomark | |
50 | |
51 **Output** | |
52 | |
53 Same as input format. | |
54 | |
55 ----- | |
56 | |
57 .. class:: infomark | |
58 | |
59 **Cite** | |
60 | |
61 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ | |
62 | |
63 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 | |
64 | |
65 `Open Babel`_ | |
66 | |
67 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page | |
68 | |
69 </help> | |
70 </tool> |