<tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" Version="0.1" >
    <description>as canonical SMILES</description>
    <requirements>
        <requirement type="package" version="2.3.2">openbabel</requirement>
    </requirements>
    <command interpreter="python">
        get_pubchem_as_smiles.py 
            -o $pubchem_smi 
            -p 4
            ## temporary hack until my Galaxy patch is committed
            > /dev/null 2>&#38;1
    </command>
    <stdio>
        <regex match="obError" 
               source="both" 
               level="fatal" 
               description="Critical Open Babel error" />
        <regex match="obWarning"
               source="both"
               level="warning"
               description="Non-critical Open Babel warning" />
        <regex match="obInfo"
               source="both"
               level="log"
               description="Open Babel Information" />
    </stdio>
    <inputs>
        <param name="infile" type="select" display="radio" size="250" label="Load all pubchem files and convert them to canonical smiles." />
    </inputs>
    <outputs>
        <data format="smi" name="pubchem_smi" />
    </outputs>
    <tests>
    </tests>
    <help>

.. class:: infomark

**What this tool does**

This tool will fetch one PubChem_ file after another and convert them to canonical SMILES. 

.. _PubChem: http://pubchem.ncbi.nlm.nih.gov/

-----

.. class:: infomark

**Output**

The output will be one large SMILES file.
  
    </help>
</tool>