|
0
|
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>
|
|
2
|
8 <![CDATA[
|
|
0
|
9 obabel
|
|
|
10 -i"${infile.ext}"
|
|
|
11 "${infile}"
|
|
|
12 -ocopy
|
|
|
13 -O "${outfile}"
|
|
|
14 --filter "atoms > $cutoff"
|
|
|
15 -e
|
|
2
|
16 2>&1
|
|
|
17 ]]>
|
|
0
|
18 </command>
|
|
|
19 <inputs>
|
|
|
20 <param name="infile" format="sdf,mol,mol2,cml,inchi,smi" type="data" label="Molecular input file" />
|
|
|
21 <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)" />
|
|
|
22 </inputs>
|
|
|
23 <outputs>
|
|
|
24 <data format_source="infile" name="outfile" />
|
|
|
25 </outputs>
|
|
|
26 <tests>
|
|
|
27 <test>
|
|
|
28 <param name="infile" ftype="smi" value="3_mol.smi" />
|
|
|
29 <param name="cutoff" value="5" />
|
|
|
30 <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" />
|
|
|
31 </test>
|
|
|
32 </tests>
|
|
|
33 <help>
|
|
2
|
34 <![CDATA[
|
|
0
|
35
|
|
|
36 .. class:: infomark
|
|
|
37
|
|
|
38 **What this tool does**
|
|
|
39
|
|
|
40 Filters a library of compounds and removes small molecules below a predefined input number of atoms.
|
|
|
41
|
|
|
42 -----
|
|
|
43
|
|
|
44 .. class:: warningmark
|
|
|
45
|
|
|
46 **Hint**
|
|
|
47
|
|
|
48 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.
|
|
|
49
|
|
|
50 -----
|
|
|
51
|
|
|
52 .. class:: infomark
|
|
|
53
|
|
|
54 **Output**
|
|
|
55
|
|
|
56 Same as input format.
|
|
|
57
|
|
|
58 -----
|
|
|
59
|
|
|
60 .. class:: infomark
|
|
|
61
|
|
|
62 **Cite**
|
|
|
63
|
|
|
64 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_
|
|
|
65
|
|
|
66 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
|
|
|
67
|
|
|
68 `Open Babel`_
|
|
|
69
|
|
|
70 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page
|
|
|
71
|
|
2
|
72 ]]>
|
|
0
|
73 </help>
|
|
|
74 </tool>
|
