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comparison get_pubchem_as_smiles.xml @ 0:cd19c3fab3a6 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/data_source/get_pubchem commit aed18d7d09e332efe57d00b33c2b8249abefaedb
author bgruening
date Wed, 22 May 2019 07:44:03 -0400
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children 4d966d5bdd17
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-1:000000000000 0:cd19c3fab3a6
1 <tool id="ctb_pubchem_download_as_smiles" name="PubChem Download" version="0.2" >
2 <description>as canonical SMILES</description>
3 <requirements>
4 <requirement type="package" version="2.4.1">openbabel</requirement>
5 <requirement type="package" version="2.7">python</requirement>
6 </requirements>
7 <stdio>
8 <regex match="obError"
9 source="both"
10 level="fatal"
11 description="Critical Open Babel error" />
12 <regex match="obWarning"
13 source="both"
14 level="warning"
15 description="Non-critical Open Babel warning" />
16 <regex match="obInfo"
17 source="both"
18 level="log"
19 description="Open Babel Information" />
20 </stdio>
21 <command>
22 <![CDATA[
23 python '$__tool_directory__/get_pubchem_as_smiles.py'
24 -o $pubchem_smi
25 -p \${GALAXY_SLOTS:-4}
26 ## temporary hack until my Galaxy patch is committed
27 > /dev/null 2>&1
28 ]]>
29 </command>
30 <inputs>
31 </inputs>
32 <outputs>
33 <data format="smi" name="pubchem_smi" />
34 </outputs>
35 <tests>
36 </tests>
37 <help>
38 <![CDATA[
39
40 .. class:: infomark
41
42 **What this tool does**
43
44 This tool will fetch one PubChem_ file after another and convert them to canonical SMILES.
45
46 .. _PubChem: http://pubchem.ncbi.nlm.nih.gov/
47
48 -----
49
50 .. class:: infomark
51
52 **Output**
53
54 The output will be one large SMILES file.
55
56 ]]>
57 </help>
58 </tool>