Mercurial > repos > bgruening > chemical_data_sources
annotate get_pubchem/get_pubchem_as_smiles.xml @ 5:c2055dd1927b draft default tip
Uploaded
| author | bgruening |
|---|---|
| date | Thu, 24 Apr 2014 13:19:33 -0400 |
| parents | 7c1f9962ac07 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" Version="0.1" > |
| 3 | 2 <description>as canonical SMILES</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.3.2">openbabel</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python"> | |
| 0 | 7 get_pubchem_as_smiles.py |
| 8 -o $pubchem_smi | |
| 5 | 9 -p "\${GALAXY_SLOTS:-4}" |
|
4
7c1f9962ac07
Add temporary hack until my galaxy stdout/stderr UTF-8 bug is fixed.
bgruening
parents:
3
diff
changeset
|
10 ## temporary hack until my Galaxy patch is committed |
|
7c1f9962ac07
Add temporary hack until my galaxy stdout/stderr UTF-8 bug is fixed.
bgruening
parents:
3
diff
changeset
|
11 > /dev/null 2>&1 |
| 3 | 12 </command> |
| 13 <stdio> | |
| 14 <regex match="obError" | |
| 15 source="both" | |
| 16 level="fatal" | |
| 17 description="Critical Open Babel error" /> | |
| 18 <regex match="obWarning" | |
| 19 source="both" | |
| 20 level="warning" | |
| 21 description="Non-critical Open Babel warning" /> | |
| 22 <regex match="obInfo" | |
| 23 source="both" | |
| 24 level="log" | |
| 25 description="Open Babel Information" /> | |
| 26 </stdio> | |
| 27 <inputs> | |
| 28 <param name="infile" type="select" display="radio" size="250" label="Load all pubchem files and convert them to canonical smiles." /> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data format="smi" name="pubchem_smi" /> | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 </tests> | |
| 35 <help> | |
| 0 | 36 |
| 37 .. class:: infomark | |
| 38 | |
| 39 **What this tool does** | |
| 40 | |
| 41 This tool will fetch one PubChem_ file after another and convert them to canonical SMILES. | |
| 42 | |
| 43 .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/ | |
| 44 | |
| 45 ----- | |
| 46 | |
| 47 .. class:: infomark | |
| 48 | |
| 49 **Output** | |
| 50 | |
| 51 The output will be one large SMILES file. | |
| 52 | |
| 3 | 53 </help> |
| 0 | 54 </tool> |