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1 <tool id="ctb_opsin" name="IUPAC name-to-structure" version="0.1">
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2 <description>converter (OPSIN)</description>
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3 <requirements>
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4 <requirement type="package" version="1.4.0">opsin</requirement>
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5 </requirements>
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6 <command>java -jar \$JAVA_JAR_PATH/opsin-1.4.0-jar-with-dependencies.jar ${radicals} "${wildcards}" -o$oformat < "${infile}" > "${outfile}" </command>
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7 <stdio>
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 <regex match="Error:" />
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11 <regex match="EXception:" />
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12 </stdio>
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13 <inputs>
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14 <param format="tabular,text" name="infile" type="data" label="IUPAC names" help="Dataset missing? See TIP below"/>
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15 <param name="oformat" type="select" label="Output format">
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16 <option value="smi">SMILES</option>
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17 <option value="cml">Chemical Markup Language</option>
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18 <option value="inchi">InChI</option>
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19 </param>
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20 <param name='radicals' type='boolean' label='Enables interpretation of radicals' truevalue='--allowRadicals' falsevalue='' />
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21 <param name='wildcards' type='boolean' label='Radicals are output as wildcard atoms' truevalue='--wildcardRadicals' falsevalue='' />
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22 </inputs>
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23 <outputs>
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24 <data format="tabular" name="outfile" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="infile" value="iupac_names.txt"/>
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29 <param name="oformat" value="smi"/>
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30 <output name="outfile" file="opsin_results.smi"/>
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31 </test>
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32 </tests>
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33 <help>
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34
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35
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36 **What it is**
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37
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38 OPSIN_ [1] is a IUPAC name-to-structure conversion tool offering high recall and precision on organic chemical nomenclature.
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39
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40 .. _Opsin: https://bitbucket.org/dan2097/opsin/overview
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41
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42 -----
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43
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44
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45 **Cite**
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46
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47 [1] Chemical Name to Structure: OPSIN, an Open Source Solution
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48 Daniel M. Lowe, Peter T. Corbett, Peter Murray-Rust, Robert C. Glen
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49 Journal of Chemical Information and Modeling 2011 51 (3), 739-753
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50
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51 http://dx.doi.org/10.1021/ci100384d
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52
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53 </help>
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54 </tool>
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