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comparison setup.xml @ 4:b43abebffad6 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:50:01 -0400
parents 644ca8dfdf28
children c7bcae9fe040
comparison
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3:4c48f2526697 4:b43abebffad6
14 14
15 ]]></command> 15 ]]></command>
16 16
17 <inputs> 17 <inputs>
18 <!-- PDB2GMX VARS --> 18 <!-- PDB2GMX VARS -->
19 <param argument="pdb_input" type="data" format='pdb' label="PDB input file."/> 19 <param argument="pdb_input" type="data" format='pdb' label="PDB input file" help="Input structure"/>
20 <param argument="water" type="select" label="Water model" help=""> 20 <param argument="water" type="select" label="Water model" help="Model for simulating water molecules in the solvent">
21 <option value="tip3p" selected="true">TIP3P</option> 21 <option value="tip3p" selected="true">TIP3P</option>
22 <option value="tip4p">TIP4P</option> 22 <option value="tip4p">TIP4P</option>
23 <option value="tips3p">TIPS3P</option> 23 <option value="tips3p">TIPS3P</option>
24 <option value="tip5p">TIP5P</option> 24 <option value="tip5p">TIP5P</option>
25 <option value="spc">SPC</option> 25 <option value="spc">SPC</option>
26 <option value="spce">SPC/E</option> 26 <option value="spce">SPC/E</option>
27 <option value="none">None</option> 27 <option value="none">None</option>
28 </param> 28 </param>
29 29
30 <param argument="ff" type="select" label="Force field"> 30 <param argument="ff" type="select" label="Force field" help="Specify a molecular force field">
31 <option value="oplsaa" selected="true">OPLS/AA</option> 31 <option value="oplsaa" selected="true">OPLS/AA</option>
32 <option value="gromos43a1">GROMOS43A1</option> 32 <option value="gromos43a1">GROMOS43A1</option>
33 <option value="amber96">AMBER96</option> 33 <option value="amber96">AMBER96</option>
34 <option value="gromos53a6">GROMOS53A6</option> 34 <option value="gromos53a6">GROMOS53A6</option>
35 <option value="amber99sb-ildn">AMBER99SB-ILDN</option> 35 <option value="amber99sb-ildn">AMBER99SB-ILDN</option>
46 </param> 46 </param>
47 47
48 <param argument="ignore_h" type="boolean" label="Ignore hydrogens" truevalue="" falsevalue="no" help="Ignore hydrogen atoms that are in the coordinate file." /> 48 <param argument="ignore_h" type="boolean" label="Ignore hydrogens" truevalue="" falsevalue="no" help="Ignore hydrogen atoms that are in the coordinate file." />
49 49
50 <!-- EDITCONF VARS --> 50 <!-- EDITCONF VARS -->
51 <param argument="box_d" type="float" label="Box dimensions in nanometers." value="0.0" min="0.0" max="10.0" help="Box dimensions" /> 51 <param argument="box_d" type="float" label="Box dimensions in nanometers" value="0.0" min="0.0" max="10.0" help="Dimensions of the box in which simulation will take place" />
52 <param argument="box_type" type="select" label="Box type" 52 <param argument="box_type" type="select" label="Box type"
53 help="triclinic is a triclinic box, cubic is a rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron. The last two are special cases of a triclinic box. The length of the three box vectors of the truncated octahedron is the shortest distance between two opposite hexagons. Relative to a cubic box with some periodic image distance, the volume of a dodecahedron with this same periodic distance is 0.71 times that of the cube, and that of a truncated octahedron is 0.77 times."> 53 help="triclinic is a triclinic box, cubic is a rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron. The last two are special cases of a triclinic box. The length of the three box vectors of the truncated octahedron is the shortest distance between two opposite hexagons. Relative to a cubic box with some periodic image distance, the volume of a dodecahedron with this same periodic distance is 0.71 times that of the cube, and that of a truncated octahedron is 0.77 times.">
54 <option value="cubic">Rectangular box with all sides equal</option> 54 <option value="cubic">Rectangular box with all sides equal</option>
55 <option value="triclinic">Triclinic</option> 55 <option value="triclinic">Triclinic</option>
56 <option value="dodecahedron">represents a rhombic dodecahedron</option> 56 <option value="dodecahedron">represents a rhombic dodecahedron</option>
57 <option value="octahedron">truncated octahedron</option> 57 <option value="octahedron">truncated octahedron</option>
58 </param> 58 </param>
59 59
60 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> 60 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
61 61
62 </inputs> 62 </inputs>
63 <outputs> 63 <outputs>
64 <data name="output1" format="top" from_work_dir="topol.top"/> 64 <data name="output1" format="top" from_work_dir="topol.top"/>
65 <data name="output2" format="gro" from_work_dir="newbox.gro"/> 65 <data name="output2" format="gro" from_work_dir="newbox.gro"/>
81 <output name="output3" file="posres.itp" ftype="itp"/> 81 <output name="output3" file="posres.itp" ftype="itp"/>
82 </test> 82 </test>
83 </tests> 83 </tests>
84 <help><![CDATA[ 84 <help><![CDATA[
85 85
86 Initial GROMACS setup. Upload a structure in PDB format and produce a topology and a structure in GRO format contained in a box of defined shape and dimensions. 86 .. class:: infomark
87
88 **What it does**
89
90 This tool performs the initial setup prior to a GROMACS simulation. This entails producing a topology from an input structure using the pdb2gmx command and also defining a simulation box with editconf.
91
92 Please note that the tool will only successfully generate a topology for residues it recognizes (i.e. standard amino acids). If the structure contains other components such as ligands, these should be separately parameterized with the AmberTools or ACPYPE tools. In this case, make sure to also use an AMBER forcefield for this tool to ensure compatability with the ligand topology.
93
94 _____
95
96 .. class:: infomark
97
98 **Input**
99
100 - PDB file.
101 - Water model and forcefield must be specified.
102 - Parameters for the simulation box (dimensions and shape).
103
104 _____
105
106
107 .. class:: infomark
108
109 **Output**
110
111 - GROMACS topology (TOP) file.
112 - Position restraint (itp) file, which may be useful for system equilibration.
113 - GRO structure file.
87 114
88 ]]></help> 115 ]]></help>
89 116
90 <expand macro="citations" /> 117 <expand macro="citations" />
91 </tool> 118 </tool>