Mercurial > repos > bgruening > opsin
view 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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<tool id="ctb_opsin" name="IUPAC name-to-structure" version="0.1"> <description>converter (OPSIN)</description> <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism> <requirements> <requirement type="package" version="1.4.0">opsin</requirement> </requirements> <command>java -jar \$JAVA_JAR_PATH/opsin-1.4.0-jar-with-dependencies.jar "${radicals}" "${wildcards}" -o$oformat < "${infile}" > "${outfile}" </command> <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> <regex match="Error:" /> <regex match="EXception:" /> </stdio> <inputs> <param format="tabular,text" name="infile" type="data" label="IUPAC names" help="Dataset missing? See TIP below"/> <param name="oformat" type="select" label="Output format"> <option value="smi">SMILES</option> <option value="cml">Chemical Markup Language</option> <option value="inchi">InChI</option> </param> <param name='radicals' type='boolean' label='Enables interpretation of radicals' truevalue='--allowRadicals' falsevalue='' /> <param name='wildcards' type='boolean' label='Radicals are output as wildcard atoms' truevalue='--wildcardRadicals' falsevalue='' /> </inputs> <outputs> <data format="smi" name="outfile"> <change_format> <when input="oformat" value="cml" format="cml"/> <when input="oformat" value="inchi" format="inchi"/> </change_format> </data> </outputs> <tests> <test> <param name="infile" value="iupac_names.txt"/> <param name="oformat" value="smi"/> <output name="outfile" file="opsin_results.smi"/> </test> </tests> <help> .. class:: infomark **What this tool does** OPSIN_ is a IUPAC name-to-structure conversion tool offering high recall and precision on organic chemical nomenclature. .. _OPSIN: https://bitbucket.org/dan2097/opsin/overview ----- .. class:: infomark **Cite** Daniel M Lowe, Peter T Corbett, Peter Murray-Rust, Robert C Glen - `Chemical Name to Structure: OPSIN, an Open Source Solution`_ .. _`Chemical Name to Structure: OPSIN, an Open Source Solution`: http://dx.doi.org/10.1021/ci100384d </help> </tool>