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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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2
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3 <requirements>
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4 <requirement type="package" version="2.3.2">openbabel</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 get_pubchem_as_smiles.py
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8 -o $pubchem_smi
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9 -p 4
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10 2>&1
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11 </command>
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12 <inputs>
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13 <param name="infile" type="select" display="radio" size="250" label="Load all pubchem files and convert them to canonical smiles." />
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14 </inputs>
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15 <outputs>
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16 <data format="smi" name="pubchem_smi" />
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17 </outputs>
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18 <tests>
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19 </tests>
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20 <help>
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21
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22 .. class:: infomark
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23
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24 **What this tool does**
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25
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26 This tool will fetch one PubChem_ file after another and convert them to canonical SMILES.
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27
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28 .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/
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29
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30 -----
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31
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32 .. class:: infomark
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33
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34 **Output**
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35
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36 The output will be one large SMILES file.
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37
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38 </help>
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39 </tool>
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