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comparison parmchk2.xml @ 0:a1a204464657 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
author chemteam
date Thu, 13 Jun 2019 03:52:29 -0400
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1 <tool id="ambertools_parmchk2" name="ParmChk2" version="@VERSION@">
2 <description>Amber's parameter checker</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <command detect_errors="exit_code">
8 <![CDATA[
9 parmchk2 -i '$input1'
10 -f '$input1.ext'
11 -s '$allparams.s'
12 -a '$allparams.a'
13 -o '$output1'
14 ]]>
15 </command>
16 <inputs>
17 <param type="data" name="input1" label="Molecular input (mol2)" format="mol2"/>
18 <section name="allparams" title="General Parameters" expanded="true">
19 <param name="s" type="select" display="radio" label="FFparm set parameter" help="(-s)">
20 <option selected="True" value="1">1: gaff</option>
21 <option value="2">2: gaff2</option>
22 </param>
23 <param name="a" type="boolean" checked="false" truevalue="Y" falsevalue="N" label="Print all force field parameters" help="(-a)"/>
24 </section>
25 </inputs>
26 <outputs>
27 <data format="txt" name="output1" label="${tool.name}: frcmod output"></data>
28 </outputs>
29 <tests>
30 <test>
31 <param name="input1" value="LigA_prmchk.mol2"/>
32 <section name="allparams">
33 <param name="s" value="2"/>
34 </section>
35 <output name="output1" file="LigA_output.txt" compare="diff" lines_diff="0"></output>
36 </test>
37 </tests>
38 <help>
39 <![CDATA[
40 .. class:: infomark
41
42 **What it does**
43
44 Antechamber parameter check reads in a mol2 file and writes out a force field modification (frcmod) file containing any force field parameters that are needed for the molecule but not supplied by the force field file.
45 Problematic parameters, if any, are indicated in the frcmod file with the note, “ATTN, need revision”, and are typically given values of zero.
46
47
48 .. class:: infomark
49
50 **How it works**
51
52 - Select a mol input file (mol2)
53 - Choose GAFF or GAFF2 parameter set
54
55 .. class:: infomark
56
57 **Outputs created**
58
59 - Outputs a frcmod file as text
60
61 .. class:: infomark
62
63 **User guide and documentation**
64
65 - AmberTools `userguide`_
66
67
68 .. _`userguide`: http://ambermd.org/doc12/Amber19.pdf
69
70 .. class:: infomark
71
72 **Feature requests**
73
74 Go to Galaxy Computational Chemistry and make a `feature request`_
75
76 .. _`feature request`: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/new
77
78 ]]>
79 </help>
80 <expand macro="citations"/>
81 </tool>