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1 <tool id="ctb_pubchem_download_assays" name="PubChem Assay Downloader" Version="0.1" >
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2 <description>as canonical SMILES</description>
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3 <command interpreter="python">
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4 get_pubchem_assay.py
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5 -o $pubchem_assay_tsv
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6 -p "\${GALAXY_SLOTS:-4}"
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7 --white-list $white_list
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8 </command>
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9 <stdio>
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10 <!-- Anything other than zero is an error -->
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11 <exit_code range="1:" />
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12 <exit_code range=":-1" />
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13 <!-- In case the return code has not been set propery check stderr too -->
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14 <regex match="Error:" />
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15 <regex match="Exception:" />
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16 </stdio>
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17 <inputs>
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18 <param name="white_list" type="select" multiple="true" label="Scoring matrix">
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19 <option value="Active" selected="true">Active</option>
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20 <option value="Inconclusive" selected="true">Inconclusive</option>
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21 <option value="Inactive">Inactive</option>
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22 <option value="Unspecified">Unspecified</option>
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23 <option value="Probe">Probe</option>
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24 </param>
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25 </inputs>
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26 <outputs>
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27 <data format="tabular" name="pubchem_assay_tsv" />
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28 </outputs>
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29 <tests>
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30 </tests>
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31 <help>
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32
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33 .. class:: infomark
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34
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35 **What this tool does**
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36
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37 This tool will fetch one PubChem_ Assay file after another and concatenating them.
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38 It is possible to optionally filter by PUBCHEM_ACTIVITY_OUTCOME.
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39
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40 Columns in the result file:
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41
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42 - column 1: PubChem AID (assay id)
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43 - column 1: PubChem SID (substance id)
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44 - column 2: PubChem CID (compound id)
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45 - column 3: PubChem Activity Outcome
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46 1-Inactive
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47 2-Active
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48 3-Inconclusive
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49 4-Unspecified
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50 5-Probe
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51 - column 4: PubChem activity score, the higher value, the more active
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52 - column 5: Test result specific comment
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53 - 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
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54
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55
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56
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57 .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/
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58
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59 -----
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60
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61 .. class:: infomark
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62
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63 **Output**
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64
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65 The output will be one large SMILES file.
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66
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67 </help>
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68 </tool>
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