Mercurial > repos > bgruening > enumerate_charges
comparison enumerate_charges.xml @ 0:0f3e5c69251e draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 20df7e562341cd30e89a14d6bde9054956fadc06"
author | bgruening |
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date | Tue, 10 Mar 2020 12:57:24 -0400 |
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children | 36360fa103d6 |
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1 <tool id="enumerate_charges" name="Enumerate changes" version="0.1"> | |
2 <description>calculated with Dimorphite DL and RDKit</description> | |
3 <requirements> | |
4 <requirement type="package" version="2019.09.2">rdkit</requirement> | |
5 </requirements> | |
6 <command detect_errors="exit_code"> | |
7 <![CDATA[ | |
8 python '$__tool_directory__/dimorphite_dl.py' | |
9 --smiles_file '$input' | |
10 --output_file '$output' | |
11 --min_ph $min_ph | |
12 --max_ph $max_ph | |
13 ]]> | |
14 </command> | |
15 <inputs> | |
16 <param name="input" format="smi" type="data" label="Input molecule data" | |
17 help="In SMILES format"/> | |
18 <param name="min_ph" type="float" label="Minimum pH" value="6.4" min="0" max="14"/> | |
19 <param name="max_ph" type="float" label="Maximum pH" value="8.4" min="0" max="14"/> | |
20 </inputs> | |
21 <outputs> | |
22 <data format="smi" name="output" /> | |
23 </outputs> | |
24 <tests> | |
25 <test> | |
26 <param name="input" ftype='smi' value="mols.smi" /> | |
27 <param name="min_ph" value="6.4" /> | |
28 <param name="max_ph" value="8.4" /> | |
29 <output name="output" ftype='smi'> | |
30 <!-- there are problems comparing the output to the expected due to whitespace differences | |
31 so we just check that the number of lines is as expected --> | |
32 <assert_contents> | |
33 <has_n_lines n="7" /> | |
34 <has_text text="NC(CCCC[NH3+])C(=O)[O-]" /> | |
35 <has_text text="NCCCCC(N)C(=O)[O-]" /> | |
36 <has_text text="NCCCCC([NH3+])C(=O)[O-]" /> | |
37 </assert_contents> | |
38 </output> | |
39 </test> | |
40 <test> | |
41 <param name="input" ftype='smi' value="mols.smi" /> | |
42 <param name="min_ph" value="4.4" /> | |
43 <param name="max_ph" value="10.4" /> | |
44 <output name="output" ftype='smi'> | |
45 <assert_contents> | |
46 <has_n_lines n="14" /> | |
47 <has_text text="NC(CCCC[NH3+])C(=O)O" /> | |
48 <has_text text="NCCCCC([NH3+])C(=O)[O-]" /> | |
49 <has_text text="NC(CCCC[NH3+])C(=O)[O-]" /> | |
50 <has_text text="NCCCCC([NH3+])C(=O)O" /> | |
51 <has_text text="NC(CCCC[NH3+])C(=O)O" /> | |
52 <has_text text="NCCCCC(N)C(=O)O" /> | |
53 </assert_contents> | |
54 </output> | |
55 </test> | |
56 </tests> | |
57 <help> | |
58 <![CDATA[ | |
59 | |
60 .. class:: infomark | |
61 | |
62 **What this tool does** | |
63 | |
64 Dimorphite DL provides rules on how to enumerate the different charge forms of molecules using RDKit. | |
65 Source code can be found here: https://git.durrantlab.pitt.edu/jdurrant/dimorphite_dl | |
66 | |
67 | |
68 ----- | |
69 | |
70 .. class:: infomark | |
71 | |
72 **Input** | |
73 | |
74 - `SMILES Format`_ | |
75 | |
76 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification | |
77 | |
78 ----- | |
79 | |
80 .. class:: infomark | |
81 | |
82 **Output** | |
83 | |
84 SMILES format with the enumerated molecules. If an ID was provided in the input this is retained in the output. | |
85 | |
86 | |
87 ]]> | |
88 </help> | |
89 <citations> | |
90 <citation type="doi">10.1186/s13321-019-0336-9</citation> | |
91 <citation type="bibtex"> | |
92 @article{rdkit, | |
93 author = {Greg Landrum and others}, | |
94 title = {RDKit: Open-source cheminformatics}, | |
95 url ={http://www.rdkit.org} | |
96 }</citation> | |
97 </citations> | |
98 </tool> |