Mercurial > repos > bgruening > chemical_data_sources
annotate get_pubchem/get_pubchem_as_smiles.xml @ 5:c2055dd1927b draft default tip
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author | bgruening |
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date | Thu, 24 Apr 2014 13:19:33 -0400 |
parents | 7c1f9962ac07 |
children |
rev | line source |
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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
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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> |