Mercurial > repos > bgruening > openbabel
comparison filter/ob_grep.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_obgrep" name="Compound Search" version="0.1"> | |
2 <description>an advanced molecular grep program using SMARTS</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 ## The command is a Cheetah template which allows some Python based syntax. | |
9 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces | |
10 obgrep | |
11 | |
12 $invert_matches | |
13 #if $n_times != 0: | |
14 -t $n_times | |
15 #end if | |
16 | |
17 $only_name | |
18 $full_match | |
19 $number_of_matches | |
20 -i ${infile.ext} | |
21 "${smarts_pattern}" | |
22 "${infile}" | |
23 > "${outfile}" 2>&1 | |
24 </command> | |
25 <inputs> | |
26 <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format."/> | |
27 <param name="smarts_pattern" type="text" format="text" label="SMARTS Pattern" help="Specify a SMARTS Pattern for your search."/> | |
28 <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules" truevalue="-v" falsevalue="" checked="false" /> | |
29 <param name="n_times" type="integer" value="0" label="Print a molecule only if the pattern occurs # times inside the molecule" /> | |
30 <param name="only_name" type="boolean" label="Only print the name of the molecules" truevalue="-n" falsevalue="" checked="false" /> | |
31 <param name="full_match" type="boolean" label="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern" truevalue="-f" falsevalue="" checked="false" /> | |
32 <param name="number_of_matches" type="boolean" label="Print the number of matches" truevalue="-c" falsevalue="" checked="false" /> | |
33 </inputs> | |
34 <options sanitize="False"/> | |
35 <outputs> | |
36 <data name="outfile" format_source="infile" label="${tool.name} on ${on_string}"/> | |
37 </outputs> | |
38 <tests> | |
39 <test> | |
40 <param name="infile" ftype="smi" value="8_mol.smi"/> | |
41 <param name="smarts_pattern" value="CO"/> | |
42 <param name="invert_matches" value="" /> | |
43 <param name="n_times" value="0"/> | |
44 <param name="only_name" value="" /> | |
45 <param name="full_match" value="" /> | |
46 <param name="number_of_matches" value="" /> | |
47 <output name="outfile" ftype="smi" file="obgrep_on_8_mol.smi"/> | |
48 </test> | |
49 </tests> | |
50 <help> | |
51 | |
52 .. class:: infomark | |
53 | |
54 **What this tool does** | |
55 | |
56 Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files. | |
57 It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_. | |
58 | |
59 | |
60 .. _Obgrep: http://openbabel.org/wiki/Obgrep | |
61 .. _here: http://openbabel.org/wiki/SMARTS | |
62 | |
63 ----- | |
64 | |
65 .. class:: infomark | |
66 | |
67 **Input** | |
68 | |
69 | - `SD-Format`_ | |
70 | - `SMILES Format`_ | |
71 | |
72 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file | |
73 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification | |
74 | |
75 ----- | |
76 | |
77 .. class:: infomark | |
78 | |
79 **Output** | |
80 | |
81 Same as input format. | |
82 | |
83 ----- | |
84 | |
85 .. class:: infomark | |
86 | |
87 **Cite** | |
88 | |
89 N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_ | |
90 | |
91 .. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33 | |
92 | |
93 `Open Babel`_ | |
94 | |
95 .. _`Open Babel`: http://openbabel.org/wiki/Main_Page | |
96 | |
97 </help> | |
98 </tool> |