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1 <tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" Version="0.1" >
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2 <description>as canonical SMILES</description>
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3 <command interpreter="python">
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4 get_pubchem_as_smiles.py
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5 -o $pubchem_smi
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6 -p 10
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7 2>&1
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8 </command>
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9 <inputs>
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10 <param name="infile" type="select" display="radio" size="250" label="Load all pubchem files and convert them to canonical smiles." />
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11 </inputs>
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12 <outputs>
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13 <data format="smi" name="pubchem_smi" />
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14 </outputs>
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15 <tests>
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16 </tests>
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17 <help>
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18
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19 .. class:: infomark
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20
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21 **What this tool does**
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22
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23 This tool will fetch one PubChem_ file after another and convert them to canonical SMILES.
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24
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25 .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/
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26
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27 -----
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28
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29 .. class:: infomark
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30
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31 **Output**
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32
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33 The output will be one large SMILES file.
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34
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35 </help>
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36 </tool>
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