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view get_pubchem/get_pubchem_assays.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 |
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<tool id="ctb_pubchem_download_assays" name="PubChem Assay Downloader" Version="0.1" > <description>as canonical SMILES</description> <command interpreter="python"> get_pubchem_assay.py -o $pubchem_assay_tsv -p "\${GALAXY_SLOTS:-4}" --white-list $white_list </command> <stdio> <!-- Anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> <!-- In case the return code has not been set propery check stderr too --> <regex match="Error:" /> <regex match="Exception:" /> </stdio> <inputs> <param name="white_list" type="select" multiple="true" label="Scoring matrix"> <option value="Active" selected="true">Active</option> <option value="Inconclusive" selected="true">Inconclusive</option> <option value="Inactive">Inactive</option> <option value="Unspecified">Unspecified</option> <option value="Probe">Probe</option> </param> </inputs> <outputs> <data format="tabular" name="pubchem_assay_tsv" /> </outputs> <tests> </tests> <help> .. class:: infomark **What this tool does** This tool will fetch one PubChem_ Assay file after another and concatenating them. It is possible to optionally filter by PUBCHEM_ACTIVITY_OUTCOME. Columns in the result file: - column 1: PubChem AID (assay id) - column 1: PubChem SID (substance id) - column 2: PubChem CID (compound id) - column 3: PubChem Activity Outcome 1-Inactive 2-Active 3-Inconclusive 4-Unspecified 5-Probe - column 4: PubChem activity score, the higher value, the more active - column 5: Test result specific comment - column 6 and beyond: All remaining columns starting from the 7th column are the TID "names" defined in the associated assay description given by the XML file under the corresponding Description/ directory. These "names" can also be found in the "Result Definitions" section of the assay summary page: e.g. http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=2244#aDefinitions .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/ ----- .. class:: infomark **Output** The output will be one large SMILES file. </help> </tool>