view get_pubchem/get_pubchem_as_smiles.xml @ 2:b65518a007fa draft

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<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
            2>&#38;1
  </command>
  <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>