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comparison restraints.xml @ 0:72c2b7992c26 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 11:14:52 -0500
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children ca6a4740114e
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-1:000000000000 0:72c2b7992c26
1 <tool id="gmx_restraints" name="Create GROMACS position restraints files" version="@VERSION@">
2 <description>using genrestr</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6
7 <expand macro="requirements" />
8
9 <command detect_errors="exit_code"><![CDATA[
10
11 ln -s '$gro_input' ./gro_input.gro &&
12 ln -s '$ndx_input' ./ndx_input.ndx &&
13 echo '$index' | gmx genrestr -f ./gro_input.gro -n ./ndx_input.ndx -o posre.itp -fc $fc &>> verbose.txt
14
15 ]]></command>
16
17 <inputs>
18 <param argument="gro_input" type="data" format='gro' label="GRO input file" help="Input structure"/>
19 <param argument="ndx_input" type="data" format='ndx' label="Index (NDX) file" help="Index file containing the atoms which should be restrained"/>
20 <param argument="fc" type="text" value="1000 1000 1000" label="Force constants" help="Vector (in Cartesian space) specifying force constants for the restraints (kJ/mol nm^2)">
21 <validator type="regex" message="Only numeric values and whitespace allowed">^[0-9 ]*$</validator>
22 </param>
23 <param argument="index" type="text" label="Index of group" help="Index of group for calculating position restraints - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).">
24 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
25 </param>
26
27 <expand macro="log" />
28
29 </inputs>
30 <outputs>
31 <data name="output1" format="itp" from_work_dir="posre.itp"/>
32 <expand macro="log_outputs" />
33 </outputs>
34 <tests>
35 <test>
36 <param name="gro_input" value="md_0_1.gro" />
37 <param name="ndx_input" value="md_0_1.ndx" />
38 <param name="fc" value="500 600 700" />
39 <param name="index" value="16" />
40 <output name="output1" file="posre_cl.itp" ftype="itp"/>
41 </test>
42 </tests>
43 <help><![CDATA[
44
45 .. class:: infomark
46
47 **What it does**
48
49 This tool calculates a position restraint (ITP) file for part of a system, specified in provided GRO and NDX files.
50
51 _____
52
53 .. class:: infomark
54
55 **Input**
56
57 - GRO structure file.
58 - Index (NDX) file.
59 - Force constant vector (in Cartesian space) for applying restraints. E.g. '1000 1000 1000' will apply a force constraint of 1000 kJ/mol nm^2 along each (XYZ) axis.
60 - Index number of the group for which restraints should be calculated, i.e. the position of the group in the index file.
61
62 _____
63
64
65 .. class:: infomark
66
67 **Output**
68
69 - Position restraint (itp) file, which may be useful for system equilibration.
70
71 ]]></help>
72
73 <expand macro="citations" />
74 </tool>