Mercurial > repos > bgruening > chemical_data_sources
view get_pubchem/get_pubchem_as_smiles.xml @ 5:c2055dd1927b draft default tip
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author | bgruening |
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date | Thu, 24 Apr 2014 13:19:33 -0400 |
parents | 7c1f9962ac07 |
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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 "\${GALAXY_SLOTS:-4}" ## temporary hack until my Galaxy patch is committed > /dev/null 2>&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>