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comparison get_pubchem/get_pubchem_as_smiles.xml @ 3:021f0ef9474f draft

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author bgruening
date Wed, 18 Sep 2013 09:44:36 -0400
parents b65518a007fa
children 7c1f9962ac07
comparison
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2:b65518a007fa 3:021f0ef9474f
1 <tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" Version="0.1" > 1 <tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" Version="0.1" >
2 <description>as canonical SMILES</description> 2 <description>as canonical SMILES</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.3.2">openbabel</requirement> 4 <requirement type="package" version="2.3.2">openbabel</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command interpreter="python">
7 get_pubchem_as_smiles.py 7 get_pubchem_as_smiles.py
8 -o $pubchem_smi 8 -o $pubchem_smi
9 -p 4 9 -p 4
10 2>&#38;1 10 </command>
11 </command> 11 <stdio>
12 <inputs> 12 <regex match="obError"
13 <param name="infile" type="select" display="radio" size="250" label="Load all pubchem files and convert them to canonical smiles." /> 13 source="both"
14 </inputs> 14 level="fatal"
15 <outputs> 15 description="Critical Open Babel error" />
16 <data format="smi" name="pubchem_smi" /> 16 <regex match="obWarning"
17 </outputs> 17 source="both"
18 <tests> 18 level="warning"
19 </tests> 19 description="Non-critical Open Babel warning" />
20 <help> 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>
21 34
22 .. class:: infomark 35 .. class:: infomark
23 36
24 **What this tool does** 37 **What this tool does**
25 38
33 46
34 **Output** 47 **Output**
35 48
36 The output will be one large SMILES file. 49 The output will be one large SMILES file.
37 50
38 </help> 51 </help>
39 </tool> 52 </tool>