Mercurial > repos > bgruening > get_pubchem
comparison get_pubchem_assays.xml @ 0:cd19c3fab3a6 draft
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 |
| parents | |
| children | 4d966d5bdd17 |
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| -1:000000000000 | 0:cd19c3fab3a6 |
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| 1 <tool id="ctb_pubchem_download_assays" name="PubChem Assay Downloader" version="0.2" > | |
| 2 <description>as table</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.7">python</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="aggressive"> | |
| 7 <![CDATA[ | |
| 8 python '$__tool_directory__/get_pubchem_assay.py' | |
| 9 -o '$pubchem_assay_tsv' | |
| 10 -p '\${GALAXY_SLOTS:-4}' | |
| 11 --white-list $white_list | |
| 12 ]]> | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param name="white_list" type="select" multiple="true" label="Scoring matrix"> | |
| 16 <option value="Active" selected="true">Active</option> | |
| 17 <option value="Inconclusive" selected="true">Inconclusive</option> | |
| 18 <option value="Inactive">Inactive</option> | |
| 19 <option value="Unspecified">Unspecified</option> | |
| 20 <option value="Probe">Probe</option> | |
| 21 </param> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data format="tabular" name="pubchem_assay_tsv" /> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 </tests> | |
| 28 <help> | |
| 29 <![CDATA[ | |
| 30 | |
| 31 .. class:: infomark | |
| 32 | |
| 33 **What this tool does** | |
| 34 | |
| 35 This tool will fetch one PubChem_ Assay file after another and concatenating them. | |
| 36 It is possible to optionally filter by PUBCHEM_ACTIVITY_OUTCOME. | |
| 37 | |
| 38 Columns in the result file: | |
| 39 | |
| 40 - column 1: PubChem AID (assay id) | |
| 41 - column 1: PubChem SID (substance id) | |
| 42 - column 2: PubChem CID (compound id) | |
| 43 - column 3: PubChem Activity Outcome | |
| 44 1-Inactive | |
| 45 2-Active | |
| 46 3-Inconclusive | |
| 47 4-Unspecified | |
| 48 5-Probe | |
| 49 - column 4: PubChem activity score, the higher value, the more active | |
| 50 - column 5: Test result specific comment | |
| 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 | |
| 52 | |
| 53 | |
| 54 | |
| 55 .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/ | |
| 56 | |
| 57 ----- | |
| 58 | |
| 59 .. class:: infomark | |
| 60 | |
| 61 **Output** | |
| 62 | |
| 63 The output will be one large SMILES file. | |
| 64 | |
| 65 ]]> | |
| 66 </help> | |
| 67 </tool> |