Mercurial > repos > bgruening > opsin
comparison opsin.xml @ 0:cda22c799d0a draft default tip
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author | bgruening |
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date | Thu, 15 Aug 2013 03:37:25 -0400 |
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-1:000000000000 | 0:cda22c799d0a |
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1 <tool id="ctb_opsin" name="IUPAC name-to-structure" version="0.1"> | |
2 <description>converter (OPSIN)</description> | |
3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism> | |
4 <requirements> | |
5 <requirement type="package" version="1.4.0">opsin</requirement> | |
6 </requirements> | |
7 <command>java -jar \$JAVA_JAR_PATH/opsin-1.4.0-jar-with-dependencies.jar "${radicals}" "${wildcards}" -o$oformat < "${infile}" > "${outfile}" </command> | |
8 <stdio> | |
9 <exit_code range="1:" /> | |
10 <exit_code range=":-1" /> | |
11 <regex match="Error:" /> | |
12 <regex match="EXception:" /> | |
13 </stdio> | |
14 <inputs> | |
15 <param format="tabular,text" name="infile" type="data" label="IUPAC names" help="Dataset missing? See TIP below"/> | |
16 <param name="oformat" type="select" label="Output format"> | |
17 <option value="smi">SMILES</option> | |
18 <option value="cml">Chemical Markup Language</option> | |
19 <option value="inchi">InChI</option> | |
20 </param> | |
21 <param name='radicals' type='boolean' label='Enables interpretation of radicals' truevalue='--allowRadicals' falsevalue='' /> | |
22 <param name='wildcards' type='boolean' label='Radicals are output as wildcard atoms' truevalue='--wildcardRadicals' falsevalue='' /> | |
23 </inputs> | |
24 <outputs> | |
25 <data format="smi" name="outfile"> | |
26 <change_format> | |
27 <when input="oformat" value="cml" format="cml"/> | |
28 <when input="oformat" value="inchi" format="inchi"/> | |
29 </change_format> | |
30 </data> | |
31 </outputs> | |
32 <tests> | |
33 <test> | |
34 <param name="infile" value="iupac_names.txt"/> | |
35 <param name="oformat" value="smi"/> | |
36 <output name="outfile" file="opsin_results.smi"/> | |
37 </test> | |
38 </tests> | |
39 <help> | |
40 | |
41 | |
42 .. class:: infomark | |
43 | |
44 **What this tool does** | |
45 | |
46 OPSIN_ is a IUPAC name-to-structure conversion tool offering high recall and precision on organic chemical nomenclature. | |
47 | |
48 .. _OPSIN: https://bitbucket.org/dan2097/opsin/overview | |
49 | |
50 ----- | |
51 | |
52 .. class:: infomark | |
53 | |
54 **Cite** | |
55 | |
56 Daniel M Lowe, Peter T Corbett, Peter Murray-Rust, Robert C Glen - `Chemical Name to Structure: OPSIN, an Open Source Solution`_ | |
57 | |
58 .. _`Chemical Name to Structure: OPSIN, an Open Source Solution`: http://dx.doi.org/10.1021/ci100384d | |
59 | |
60 | |
61 </help> | |
62 </tool> |