comparison get_pubchem/get_pubchem_assays.xml @ 5:c2055dd1927b draft default tip

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5:c2055dd1927b

<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>