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comparison ob_addh.xml @ 0:ada6daa717d2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author bgruening
date Sat, 20 May 2017 08:37:26 -0400
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children d2e6d682bcd0
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-1:000000000000 0:ada6daa717d2
1 <tool id="openbabel_addh" name="Add hydrogen atoms" version="@VERSION@.0">
2 <description>at a certain pH value</description>
3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="aggressive">
9 <![CDATA[
10 python $__tool_directory__/ob_addh.py
11 -i "${infile}"
12 --iformat "${infile.ext}"
13 -o "${outfile}"
14 $polar
15 --pH "${pH_value}"
16 ]]>
17 </command>
18 <inputs>
19 <expand macro="infile_all_types"/>
20 <param name="polar" type="boolean" truevalue="--polar" falsevalue="" label="Add hydrogens to polar atoms only"/>
21 <param name="pH_value" type="float" value="7.4" min="0" max="14" label="Specify pH value"/>
22 </inputs>
23 <outputs>
24 <expand macro="output_like_input"/>
25 </outputs>
26 <tests>
27 <test>
28 <param name="infile" value="CID_2244.can" ftype="smi" />
29 <param name="polar" value="--polar" />
30 <param name="pH_value" value="7.4" />
31 <output name="outfile" file="CID_2244_addh.can" ftype="smi" />
32 </test>
33 </tests>
34 <help>
35 <![CDATA[
36
37 .. class:: infomark
38
39 **What this tool does**
40
41 Parses a molecular file and adds hydrogen atoms at a user-defined pH value.
42
43 * Protocol::
44
45 1. The hydrogen atoms included in the input molecule are deleted.
46 2. Protonation state is predicted at the target pH and the corresponding hydrogen atoms added accordingly.
47
48 -----
49
50 .. class:: infomark
51
52 **Input**
53
54 3D format files are required, e.g. SDF_
55
56 .. _SDF: http://en.wikipedia.org/wiki/Chemical_table_file
57
58 -----
59
60 .. class:: warningmark
61
62 **Hint**
63
64 To avoid possible crashes, only molecules with more than five heavy atoms are parsed.
65
66 -----
67
68 .. class:: infomark
69
70 **Output**
71
72 Same output format as the input format.
73
74
75 ]]>
76 </help>
77 <expand macro="citations">
78 <citation type="doi">10.1186/1752-153X-2-5</citation>
79 </expand>
80 </tool>