Mercurial > repos > bgruening > opsin
annotate opsin.xml @ 11:ee73c8d529b1 default tip
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Tue, 23 Jul 2013 14:54:46 +0200 |
| parents | 96e5c3da1870 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="ctb_opsin" name="IUPAC name-to-structure" version="0.1"> |
| 2 <description>converter (OPSIN)</description> | |
| 3 | 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism> |
| 0 | 4 <requirements> |
| 5 <requirement type="package" version="1.4.0">opsin</requirement> | |
| 6 </requirements> | |
|
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96e5c3da1870
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
6
diff
changeset
|
7 <command>java -jar \$JAVA_JAR_PATH/opsin-1.4.0-jar-with-dependencies.jar "${radicals}" "${wildcards}" -o$oformat < "${infile}" > "${outfile}" </command> |
| 0 | 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> | |
| 6 | 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> | |
| 0 | 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 | |
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9
96e5c3da1870
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
6
diff
changeset
|
42 .. class:: infomark |
|
96e5c3da1870
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
6
diff
changeset
|
43 |
|
96e5c3da1870
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
6
diff
changeset
|
44 **What this tool does** |
| 0 | 45 |
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96e5c3da1870
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
6
diff
changeset
|
46 OPSIN_ is a IUPAC name-to-structure conversion tool offering high recall and precision on organic chemical nomenclature. |
| 0 | 47 |
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96e5c3da1870
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
6
diff
changeset
|
48 .. _OPSIN: https://bitbucket.org/dan2097/opsin/overview |
| 0 | 49 |
| 50 ----- | |
| 51 | |
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96e5c3da1870
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
6
diff
changeset
|
52 .. class:: infomark |
| 0 | 53 |
| 54 **Cite** | |
| 55 | |
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96e5c3da1870
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
6
diff
changeset
|
56 Daniel M Lowe, Peter T Corbett, Peter Murray-Rust, Robert C Glen - `Chemical Name to Structure: OPSIN, an Open Source Solution`_ |
| 0 | 57 |
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9
96e5c3da1870
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
6
diff
changeset
|
58 .. _`Chemical Name to Structure: OPSIN, an Open Source Solution`: http://dx.doi.org/10.1021/ci100384d |
|
96e5c3da1870
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
6
diff
changeset
|
59 |
| 0 | 60 |
| 61 </help> | |
| 62 </tool> |