annotate opsin.xml @ 0:cda22c799d0a draft default tip

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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$oformat &lt; "${infile}" &gt; "${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>