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comparison get_pubchem/get_pubchem_as_smiles.xml @ 0:f653fd06f055 draft

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author bgruening
date Thu, 15 Aug 2013 03:23:17 -0400
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-1:000000000000 0:f653fd06f055
1 <tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" Version="0.1" >
2 <description>as canonical SMILES</description>
3 <command interpreter="python">
4 get_pubchem_as_smiles.py
5 -o $pubchem_smi
6 -p 10
7 2>&#38;1
8 </command>
9 <inputs>
10 <param name="infile" type="select" display="radio" size="250" label="Load all pubchem files and convert them to canonical smiles." />
11 </inputs>
12 <outputs>
13 <data format="smi" name="pubchem_smi" />
14 </outputs>
15 <tests>
16 </tests>
17 <help>
18
19 .. class:: infomark
20
21 **What this tool does**
22
23 This tool will fetch one PubChem_ file after another and convert them to canonical SMILES.
24
25 .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/
26
27 -----
28
29 .. class:: infomark
30
31 **Output**
32
33 The output will be one large SMILES file.
34
35 </help>
36 </tool>