Mercurial > repos > chemteam > ambertools_antechamber
comparison antechamber.xml @ 0:c01897428864 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 30f274b0c065dc842ca4e04aa34879443de60bcc
author | chemteam |
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date | Thu, 13 Jun 2019 03:52:54 -0400 |
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children | 59a0424937cc |
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1 <tool id="ambertools_antechamber" name="AnteChamber" version="@VERSION@"> | |
2 <description>Amber's molecular input file processor</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"></expand> | |
7 <command detect_errors="exit_code"> | |
8 <![CDATA[ | |
9 antechamber -i '$input1' | |
10 -o '$output1' | |
11 -fi '$input1.ext' | |
12 -fo '$selected_output_format' | |
13 -c '$allparams.c' | |
14 -pf '$extraparams.pf' | |
15 #if '$extraparams.usenc' | |
16 -nc '$allparams.nc' | |
17 #end if | |
18 -at '$allparams.at' | |
19 -j '$allparams.j' | |
20 -rn '$allparams.resname' | |
21 -m '$allparams.m' | |
22 ]]> | |
23 </command> | |
24 <inputs> | |
25 <param type="data" name="input1" label="Molecular input (PDB or mol2)" format="pdb,mol2"/> | |
26 <param name="selected_output_format" type="select" label="Select an output file format (mol2 recommended!):"> | |
27 <option value="pdb">pdb</option> | |
28 <option value="mol2" selected="true">mol2</option> | |
29 </param> | |
30 <section name="allparams" title="General Parameters" expanded="true"> | |
31 <param name="nc" type="integer" value="0" label="Net charge" min="-50" max="50" help="Specify the net charge for the molecule. Default is 0. (-nc)"/> | |
32 <param name="m" type="integer" value="1" label="Multiplicity" min="1" max="10" help="Multiplicity, 2S+1. Default is 1. (-m)"/> | |
33 <param name="resname" type="text" value="MOL" label="Residue name" help="From 1-3 characters allowed. Default is MOL. (-rn)"/> | |
34 <param name="c" type="select" label="Charge method" help="Charge method to use for the calculations. AM1-BCC or RESP recommended (-c)"> | |
35 <option value="resp">RESP</option> | |
36 <option selected="True" value="bcc">AM1-BCC</option> | |
37 <option value="cm1">CM1</option> | |
38 <option value="cm2">CM2</option> | |
39 <option value="esp">ESP (Kollman)</option> | |
40 <option value="mul">Mulliken</option> | |
41 <option value="gas">Gasteiger</option> | |
42 </param> | |
43 <param name="at" type="select" label="Atom type" help="Create atom type for the specified forcefield (-at)"> | |
44 <option selected="True" value="gaff">gaff</option> | |
45 <option value="gaff2">gaff2</option> | |
46 <option value="amber">amber for PARM94/99/99SB</option> | |
47 <option value="bcc">bcc</option> | |
48 <option value="sybyl">sybyl</option> | |
49 </param> | |
50 <param name="j" type="select" label="Atom type and bond type prediction index" help="Specify how to run predictions (-j)"> | |
51 <option value="0">0 - No assignment</option> | |
52 <option value="1">1 - atom type</option> | |
53 <option value="2">2 - full bond types</option> | |
54 <option value="3">3 - part bond types</option> | |
55 <option selected="True" value="4">4 - atom and full bond type (default)</option> | |
56 <option value="5">5 - atom and part bond type</option> | |
57 </param> | |
58 </section> | |
59 <section name="extraparams" title="Additional Parameters" expanded="false"> | |
60 <param name="pf" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="remove intermediate files (recommended)" help="(-pf)"/> | |
61 <param name="usenc" type="boolean" checked="true" truevalue="True" falsevalue="False" label="use netcharge (recommended)" help="Can choose to let the charge be inferred by setting this to False."/> | |
62 </section> | |
63 </inputs> | |
64 <outputs> | |
65 <data format="mol2" name="output1" label="${tool.name}: structure output"> | |
66 <change_format> | |
67 <when input="selected_output_format" value="pdb" format="pdb"/> | |
68 <when input="selected_output_format" value="mol2" format="mol2"/> | |
69 <!-- <when input="selected_format" value="xyz" format="xyz"/> <when input="selected_format" value="tinker" format="tinker"/> <when input="selected_format" value="moldy" format="moldy"/> --> | |
70 </change_format> | |
71 </data> | |
72 </outputs> | |
73 <tests> | |
74 <test> | |
75 <param name="input1" value="LigA.mol2"/> | |
76 <section name="allparams"> | |
77 <param name="nc" value="-2"/> | |
78 <param name="c" value="AM1-BCC"/> | |
79 <param name="at" value="gaff2"/> | |
80 <param name="j" value="5 - atom and part bond type"/> | |
81 </section> | |
82 <output name="output1" file="LigA_output.mol2" compare="diff" lines_diff="0"> | |
83 <assert_contents> | |
84 <has_text text=" 1 C 49.2110 26.9920 85.5530 c2 1 MOL"/> | |
85 </assert_contents> | |
86 </output> | |
87 </test> | |
88 <test> | |
89 <param name="input1" value="LigA.pdb" ftype="pdb"/> | |
90 <param name="selected_output_format" value="pdb"/> | |
91 <section name="allparams"> | |
92 <param name="nc" value="-2"/> | |
93 <param name="c" value="AM1-BCC"/> | |
94 <param name="at" value="gaff2"/> | |
95 <param name="j" value="5 - atom and part bond type"/> | |
96 </section> | |
97 <output name="output1" file="LigA_output.pdb" compare="diff" lines_diff="0"> | |
98 <assert_contents> | |
99 <has_text text="ATOM 1 C MOL 1 49.211 26.992 85.553 1.00 0.00 C"/> | |
100 </assert_contents> | |
101 </output> | |
102 </test> | |
103 </tests> | |
104 <help> | |
105 <![CDATA[ | |
106 .. class:: infomark | |
107 | |
108 **What it does** | |
109 | |
110 Antechamber sets up parameters for the input molecules provided. | |
111 | |
112 .. class:: infomark | |
113 | |
114 **How it works** | |
115 | |
116 - Select an input file (PDB, mol2) | |
117 - Specify the correct charge, or keep the default charge of 0 | |
118 - Adjust other parameters as needed. | |
119 - Click on Execute | |
120 | |
121 .. class:: infomark | |
122 | |
123 **Outputs created** | |
124 | |
125 - A mol2 or PDB output is created with the forcefield compatible atom names. | |
126 | |
127 .. class:: infomark | |
128 | |
129 **User guide and documentation** | |
130 | |
131 - AmberTools `userguide`_ | |
132 | |
133 | |
134 .. _`userguide`: http://ambermd.org/doc12/Amber19.pdf | |
135 | |
136 .. class:: infomark | |
137 | |
138 **Feature requests** | |
139 | |
140 Go to Galaxy Computational Chemistry and make a `feature request`_ | |
141 | |
142 .. _`feature request`: https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/new | |
143 | |
144 | |
145 ]]> | |
146 </help> | |
147 <expand macro="citations"/> | |
148 </tool> |