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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors commit ae026d4ea6fe2ebaa53611b86f9047941c7b899b"
author chemteam
date Thu, 27 Jan 2022 18:16:37 +0000
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1 <tool id="gromacs_modify_topology" name="Adding New Topology Information" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.09">
2 <description>to a GROMACS topology file</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 #if $str($functionality.what2add) == "mol":
10 python3 '$__tool_directory__/gmxtras_add_newmolparam.py'
11 --top_file '$functionality.inputtopology'
12 --atom_file '$functionality.nonbondparam'
13 --mol_file '$functionality.bondparam'
14 --out '$newtop'
15 #end if
16
17 #if $str($functionality.what2add) == "restraints":
18 python3 '$__tool_directory__/gmxtras_add_restraints.py'
19 --top_file '$functionality.inputtopology'
20 --res_file '$functionality.posres'
21 --molecule '$functionality.targetmolecule'
22 --out '$newtop'
23 #end if
24
25 #if $str($functionality.what2add) == "both":
26 python3 '$__tool_directory__/gmxtras_add_restraints.py'
27 --top_file '$functionality.inputtopology'
28 --res_file '$functionality.posres'
29 --molecule '$functionality.targetmolecule'
30 --out 'odoylerules'
31 &&
32 python3 '$__tool_directory__/gmxtras_add_newmolparam.py'
33 --top_file 'odoylerules'
34 --atom_file '$functionality.nonbondparam'
35 --mol_file '$functionality.bondparam'
36 --out '$newtop'
37 #end if
38
39 ]]></command>
40 <inputs>
41
42 <conditional name="functionality">
43 <param name="what2add" type="select" label="What new information are you adding to your topology file?">
44 <option value="mol">A molecule's parameters</option>
45 <option value="restraints">Position restraint information</option>
46 <option value="both">Both a molecule's topology information and position restrain information</option>
47 </param>
48 <when value="mol">
49 <param name="inputtopology" type="data" format="top" label="GROMACS Topology file to be modified" help="Topology file with missing information"/>
50 <param name="nonbondparam" type="data" format="txt" label="Atom Types with Nonbonded Parameters" help="Atom types information from grep"/>
51 <param name="bondparam" type="data" format="txt,itp" label="Molecule type information with bonded parameters" help="molecule type information"/>
52 </when>
53 <when value="restraints">
54 <param name="inputtopology" type="data" format="top" label="GROMACS Topology file to be modified" help="Topology file with missing information"/>
55 <param name="posres" type="data" format="itp" label="Position restraint file" help="Position restraint file created previously"/>
56 <param name="targetmolecule" type="text" label="Target molecule type" help="The molecule type name to which the restraints were applied"/>
57 </when>
58 <when value="both">
59 <param name="inputtopology" type="data" format="top" label="GROMACS Topology file to be modified" help="Topology file with missing information"/>
60 <param name="nonbondparam" type="data" format="txt" label="Atom Types with Nonbonded Parameters" help="Atom types information from grep"/>
61 <param name="bondparam" type="data" format="txt,itp" label="Molecule type information with bonded parameters" help="molecule type information"/>
62 <param name="posres" type="data" format="itp" label="Position restraint file" help="Position restraint file created previously"/>
63 <param name="targetmolecule" type="text" label="Target molecule type" help="The molecule type name to which the restraints were applied"/>
64 </when>
65
66 </conditional>
67 </inputs>
68 <outputs>
69 <data name="newtop" format="top" label="Modified file with new topology information ${on_string}"/>
70 </outputs>
71 <tests>
72 <test>
73 <conditional name="functionality">
74 <param name="what2add" value="mol" />
75 <param name="inputtopology" value="cid1_GMX.top" />
76 <param name="nonbondparam" value="water_nonbondedparams.itp" />
77 <param name="bondparam" value="water_bondedparams.itp" />
78 </conditional>
79 <output name="newtop">
80 <assert_contents>
81 <has_text text="HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00"/>
82 <has_text text=" 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800"/>
83 </assert_contents>
84 </output>
85 </test>
86 <test>
87 <conditional name="functionality">
88 <param name="what2add" value="restraints" />
89 <param name="inputtopology" value="cid1_GMX.top" />
90 <param name="targetmolecule" value="cid1" />
91 <param name="posres" value="posres_cid1.itp" />
92 </conditional>
93 <output name="newtop">
94 <assert_contents>
95 <has_text text="; i funct fcx fcy fcz"/>
96 <has_text text=" 42 1 1000 1000 1000"/>
97 </assert_contents>
98 </output>
99 </test>
100 <test>
101 <conditional name="functionality">
102 <param name="what2add" value="both" />
103 <param name="inputtopology" value="cid1_GMX.top" />
104 <param name="nonbondparam" value="water_nonbondedparams.itp" />
105 <param name="bondparam" value="water_bondedparams.itp" />
106 <param name="targetmolecule" value="cid1" />
107 <param name="posres" value="posres_cid1.itp" />
108 </conditional>
109 <output name="newtop">
110 <assert_contents>
111 <has_text text="HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00"/>
112 <has_text text=" 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800"/>
113 <has_text text="; i funct fcx fcy fcz"/>
114 <has_text text=" 42 1 1000 1000 1000"/>
115 </assert_contents>
116 </output>
117 </test>
118 </tests>
119 <help><![CDATA[
120
121 Tool to modify and add new information to GROMACS topology files. This is particularly useful when working with systems
122 that were created outside of GROMACS (for example, files created in AMBER or CHARMM and then converted over via acpype).
123 This tool can also be used to complement the "gmx insert-molecules" tool, which currently only modifies the GROMACS
124 structure files (gro) and requires further modification of the topology file for the newly populated system to be simulation ready.
125
126 .. class:: infomark
127
128 **Input**
129
130 1) The system topology file you are modifying,
131
132 2) a position restraint file (posres.itp) and specifying the name of the target molecule type you are restraining,
133
134 3) a molecule's atom types/nonbonded parameters to be inserted under the system's global [ atomtypes ], as well as
135
136 4) the corresponding bonded parameters of that particular molecule found under [ moleculetype ].
137
138 .. class:: infomark
139
140 **Outputs**
141
142 The new modified GROMACS topology file.
143
144
145 ]]></help>
146 <expand macro="citations">
147 <citation type="doi">doi:10.1186/1756-0500-5-367</citation>
148 </expand>
149 </tool>