Mercurial > repos > bgruening > get_pubchem

annotate get_pubchem_assays.xml @ 0:cd19c3fab3a6 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
author bgruening
date Wed, 22 May 2019 07:44:03 -0400
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cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
bgruening
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1 <tool id="ctb_pubchem_download_assays" name="PubChem Assay Downloader" version="0.2" >
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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2 <description>as table</description>
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3 <requirements>
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4 <requirement type="package" version="2.7">python</requirement>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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5 </requirements>
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6 <command detect_errors="aggressive">
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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7 <![CDATA[
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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8 python '$__tool_directory__/get_pubchem_assay.py'
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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9 -o '$pubchem_assay_tsv'
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10 -p '\${GALAXY_SLOTS:-4}'
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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11 --white-list $white_list
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param name="white_list" type="select" multiple="true" label="Scoring matrix">
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16 <option value="Active" selected="true">Active</option>
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17 <option value="Inconclusive" selected="true">Inconclusive</option>
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18 <option value="Inactive">Inactive</option>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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19 <option value="Unspecified">Unspecified</option>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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20 <option value="Probe">Probe</option>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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21 </param>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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22 </inputs>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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23 <outputs>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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24 <data format="tabular" name="pubchem_assay_tsv" />
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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25 </outputs>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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26 <tests>
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27 </tests>
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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28 <help>
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29 <![CDATA[
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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30
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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31 .. class:: infomark
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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32
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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33 **What this tool does**
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34
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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35 This tool will fetch one PubChem_ Assay file after another and concatenating them.
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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36 It is possible to optionally filter by PUBCHEM_ACTIVITY_OUTCOME.
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37
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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38 Columns in the result file:
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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39
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40 - column 1: PubChem AID (assay id)
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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41 - column 1: PubChem SID (substance id)
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42 - column 2: PubChem CID (compound id)
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43 - column 3: PubChem Activity Outcome
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44 1-Inactive
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45 2-Active
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46 3-Inconclusive
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47 4-Unspecified
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48 5-Probe
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49 - column 4: PubChem activity score, the higher value, the more active
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50 - column 5: Test result specific comment
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51 - 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
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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52
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cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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55 .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/
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57 -----
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58
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59 .. class:: infomark
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60
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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61 **Output**
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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62
cd19c3fab3a6 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
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63 The output will be one large SMILES file.
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64
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65 ]]>
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66 </help>
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67 </tool>