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comparison setup.xml @ 6:811e12c235e1 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author chemteam
date Wed, 20 Nov 2019 16:09:19 +0000
parents b4a5cd662f89
children 73d69aacd864
comparison
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5:199d20d13c3a 6:811e12c235e1
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 8
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 10
11 ln -s '$pdb_input' ./pdb_input.pdb && 11 ln -s '$pdb_input' ./pdb_input.pdb &&
12 gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water $water -ff $ff -${ignore_h}ignh &>> verbose.txt && 12 gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water $water -ff $ff -${ignore_h}ignh -merge all &>> verbose.txt
13 gmx editconf -f processed.gro -o newbox.gro -c -d $box_d -bt $box_type &>> verbose.txt
14 13
15 ]]></command> 14 ]]></command>
16 15
17 <inputs> 16 <inputs>
18 <!-- PDB2GMX VARS -->
19 <param argument="pdb_input" type="data" format='pdb' label="PDB input file" help="Input structure"/> 17 <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="Model for simulating water molecules in the solvent"> 18 <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> 19 <option value="tip3p" selected="true">TIP3P</option>
22 <option value="tip4p">TIP4P</option> 20 <option value="tip4p">TIP4P</option>
23 <option value="tips3p">TIPS3P</option> 21 <option value="tips3p">TIPS3P</option>
44 <option value="amber99">AMBER99</option> 42 <option value="amber99">AMBER99</option>
45 <option value="amber94">AMBER94</option> 43 <option value="amber94">AMBER94</option>
46 </param> 44 </param>
47 45
48 <param argument="ignore_h" type="boolean" label="Ignore hydrogens" truevalue="" falsevalue="no" help="Ignore hydrogen atoms that are in the coordinate file." /> 46 <param argument="ignore_h" type="boolean" label="Ignore hydrogens" truevalue="" falsevalue="no" help="Ignore hydrogen atoms that are in the coordinate file." />
49
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="Dimensions of the box in which simulation will take place" />
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.">
54 <option value="cubic">Rectangular box with all sides equal</option>
55 <option value="triclinic">Triclinic</option>
56 <option value="dodecahedron">represents a rhombic dodecahedron</option>
57 <option value="octahedron">truncated octahedron</option>
58 </param>
59 47
60 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/> 48 <expand macro="log" />
61 49
62 </inputs> 50 </inputs>
63 <outputs> 51 <outputs>
64 <data name="output1" format="top" from_work_dir="topol.top"/> 52 <data name="output1" format="top" from_work_dir="topol.top"/>
65 <data name="output2" format="gro" from_work_dir="newbox.gro"/> 53 <data name="output2" format="gro" from_work_dir="processed.gro"/>
66 <data name="output3" format="itp" from_work_dir="posres.itp"/> 54 <data name="output3" format="itp" from_work_dir="posres.itp"/>
67 <data name="report" format="txt" from_work_dir="verbose.txt"> 55 <expand macro="log_outputs" />
68 <filter>capture_log</filter>
69 </data>
70 </outputs> 56 </outputs>
71 <tests> 57 <tests>
72 <test> 58 <test>
73 <param name="pdb_input" value="1AKI.pdb" /> 59 <param name="pdb_input" value="1AKI.pdb" />
74 <param name="water" value="spce" /> 60 <param name="water" value="spce" />
75 <param name="ff" value="oplsaa" /> 61 <param name="ff" value="oplsaa" />
76 <param name="ignore_h" value="no" /> 62 <param name="ignore_h" value="no" />
77 <param name="box_d" value="1.0" /> 63 <param name="box_d" value="1.0" />
78 <param name="box_type" value="cubic" /> 64 <param name="box_type" value="cubic" />
79 <output name="output1" file="topol.top" ftype="top" compare="diff" lines_diff="20"/> 65 <output name="output1" file="topol.top" ftype="top" compare="diff" lines_diff="20"/>
80 <output name="output2" file="newbox.gro" ftype="gro"/> 66 <output name="output2" file="processed.gro" ftype="gro"/>
81 <output name="output3" file="posres.itp" ftype="itp"/> 67 <output name="output3" file="posres.itp" ftype="itp"/>
82 </test> 68 </test>
83 </tests> 69 </tests>
84 <help><![CDATA[ 70 <help><![CDATA[
85 71
86 .. class:: infomark 72 .. class:: infomark
87 73
88 **What it does** 74 **What it does**
89 75
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. 76 This tool performs the initial setup prior to a GROMACS simulation. This entails producing a topology from an input structure using the pdb2gmx command.
91 77
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. 78 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 79
94 _____ 80 _____
95 81
97 83
98 **Input** 84 **Input**
99 85
100 - PDB file. 86 - PDB file.
101 - Water model and forcefield must be specified. 87 - Water model and forcefield must be specified.
102 - Parameters for the simulation box (dimensions and shape).
103 88
104 _____ 89 _____
105 90
106 91
107 .. class:: infomark 92 .. class:: infomark