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
|
2
|
9 -p 4
|
3
|
10 </command>
|
|
11 <stdio>
|
|
12 <regex match="obError"
|
|
13 source="both"
|
|
14 level="fatal"
|
|
15 description="Critical Open Babel error" />
|
|
16 <regex match="obWarning"
|
|
17 source="both"
|
|
18 level="warning"
|
|
19 description="Non-critical Open Babel warning" />
|
|
20 <regex match="obInfo"
|
|
21 source="both"
|
|
22 level="log"
|
|
23 description="Open Babel Information" />
|
|
24 </stdio>
|
|
25 <inputs>
|
|
26 <param name="infile" type="select" display="radio" size="250" label="Load all pubchem files and convert them to canonical smiles." />
|
|
27 </inputs>
|
|
28 <outputs>
|
|
29 <data format="smi" name="pubchem_smi" />
|
|
30 </outputs>
|
|
31 <tests>
|
|
32 </tests>
|
|
33 <help>
|
0
|
34
|
|
35 .. class:: infomark
|
|
36
|
|
37 **What this tool does**
|
|
38
|
|
39 This tool will fetch one PubChem_ file after another and convert them to canonical SMILES.
|
|
40
|
|
41 .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/
|
|
42
|
|
43 -----
|
|
44
|
|
45 .. class:: infomark
|
|
46
|
|
47 **Output**
|
|
48
|
|
49 The output will be one large SMILES file.
|
|
50
|
3
|
51 </help>
|
0
|
52 </tool>
|