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"planemo upload for repository https://github.com/chembl/chembl_webresource_client commit 78f2261af4e00c830ea311337d0aed9b297aad8e-dirty"
author bgruening
date Sat, 10 Oct 2020 09:43:40 +0000
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1 <tool id="chembl_structure_pipeline" name="ChEMBL structure pipeline" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>for curation and standardizing of molecular structures</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.0.0</token>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">chembl_structure_pipeline</requirement>
9 </requirements>
10 <command><![CDATA[
11 python '$__tool_directory__/structure_pipeline.py'
12 --input '$input'
13 --output '$output'
14 $standardize
15 $get_parent
16 $check
17 ]]>
18 </command>
19 <inputs>
20 <param label="SDF/MOL input" type="data" name="input" format="sdf,mol" argument="--input"/>
21 <param label="Standardize" checked="false" type="boolean" name="standardize" argument="--standardize" truevalue="--standardize" falsevalue="" help="Apply the 'Standardize' pipeline component"/>
22 <param label="Get parent" checked="false" type="boolean" name="get_parent" argument="--get_parent" truevalue="--get_parent" falsevalue="" help="Apply the 'GetParent' pipeline component"/>
23 <param label="Check" checked="false" type="boolean" name="check" argument="--check" truevalue="--check" falsevalue="" help="Apply the 'Check' pipeline component"/>
24 </inputs>
25 <outputs>
26 <data name="output" format="sdf" label="Processed molecules"/>
27 </outputs>
28 <tests>
29 <test>
30 <param name="input" value="o_molblock.mol" />
31 <param name="standardize" value="true" />
32 <output name="output" value="std_molblock.mol"/>
33 </test>
34 <test>
35 <param name="input" value="o_molblock.mol" ftype="mol" />
36 <param name="get_parent" value="true" />
37 <output name="output" value="parent_molblock.mol"/>
38 </test>
39 <test>
40 <param name="input" value="o_molblock.mol" ftype="mol" />
41 <param name="check" value="true" />
42 <output name="output" value="check.mol"/>
43 </test>
44 <test>
45 <param name="input" value="10mol.sdf" ftype="sdf" />
46 <param name="standardize" value="true" />
47 <param name="get_parent" value="true" />
48 <param name="check" value="true" />
49 <output name="output" value="pipeline_multi.sdf"/>
50 </test>
51 </tests>
52 <help><![CDATA[
53
54 Apply the ChEMBL chemical curation pipeline to a set of chemical structures in SDF
55 format. The pipeline is described in detail in the citation provided (Bento et al.,
56 2020).
57
58 The pipeline consists of three components:
59 - a Standardizer which formats compounds according to defined rules and conventions, based mostly on FDA/IUPAC guidelines.
60 - a GetParent component that removes any salts and solvents from the compound to create its parent.
61 - a Checker to test the validity of chemical structures and flag any serious errors. Errors are given a code from 0 (least serious) to 10 (most serious), the highest of which is stored in the SDF field `<MaxPenaltyScore>`. A list of all errors encountered is recorded under `<IssueMessages>`.
62
63 Either one or more of these protocols can be applied in a single Galaxy job.
64
65 -----
66
67 .. class:: infomark
68
69 **Input**
70
71 One or more molecules in MOL/SDF format.
72
73 -----
74
75 .. class:: infomark
76
77 **Output**
78
79 A MOL/SD-file containing the processed molecules.
80
81 ]]></help>
82 <citations>
83 <citation type="doi">10.1186/s13321-020-00456-1</citation>
84 </citations>
85 </tool>