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comparison merge_top.xml @ 8:06ea4e040d45 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 71a3084d6e402b31563b1662bb629d5a959ce7b7"
author chemteam
date Wed, 15 Apr 2020 14:35:17 -0400
parents f2faba46d680
children ced8ec975548
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7:8ddd75c21cbd 8:06ea4e040d45
1 <tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="@VERSION@"> 1 <tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="@VERSION@">
2 <description>for example, for protein and ligand files</description> 2 <description>and GRO files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <token name="@VERSION@">3.2.0</token>
5 </macros> 5 </macros>
6 <requirements>
7 <requirement type="package" version="@VERSION@">parmed</requirement>
8 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
7 ln -s '$top_input' ./top_input.top && 10 python '$__tool_directory__/merge_top.py'
8 #for $itp_input in $itp_inputs 11 --lig-top $lig_top
9 ln -s '$itp_input' ./$itp_input.element_identifier && 12 --prot-top $prot_top
10 echo '$itp_input.element_identifier' >> ./itps.txt && 13 --lig-gro $lig_gro
11 #end for 14 --prot-gro $prot_gro
12 15 --complex-top complex.top
13 python '$__tool_directory__/merge_top.py' top_input.top itps.txt 16 --complex-gro complex.gro
14 ]]></command> 17 ]]></command>
15 <inputs> 18 <inputs>
16 <param name="top_input" type="data" format='top' label="Topology (TOP) file" help="'Master' topology into which subordinate topologies will be added."/> 19 <param name="prot_top" type="data" format='top' label="Protein topology (TOP) file" help="Protein topology into which a ligand topology will be added."/>
17 <param name="itp_inputs" type="data" format='top,itp' multiple="true" label="Topologies (TOP or ITP)" help="One or more topologies for insertion into the main topology. Either TOP or ITP format. Can include position restraint files."/> 20 <param name="lig_top" type="data" format='top,itp' label="Ligand topology (TOP or ITP) file" help="Ligand topology for insertion into the protein topology. Either TOP or ITP format."/>
21 <param name="prot_gro" type="data" format='gro' label="Protein structure (GRO) file" help="Protein structure in GRO format."/>
22 <param name="lig_gro" type="data" format='gro' label="Ligand structure (GRO) file" help="Ligand structure in GRO format."/>
18 </inputs> 23 </inputs>
19 <outputs> 24 <outputs>
20 <data name="output" format="top" from_work_dir="top_output.top"/> 25 <data name="complex_top" format="top" from_work_dir="complex.top"/>
26 <data name="complex_gro" format="gro" from_work_dir="complex.gro"/>
21 </outputs> 27 </outputs>
22 <tests> 28 <tests>
23 <test> 29 <test>
24 <param name="top_input" value="topol.top" /> 30 <param name="prot_top" value="topol.top" />
25 <param name="itp_inputs" value="posres.itp" /> 31 <param name="lig_top" value="lig.itp" />
26 <output name="output" file="top_output.top" ftype="top" /> 32 <param name="prot_gro" value="newbox.gro" />
33 <param name="lig_gro" value="lig.gro" />
34 <output name="complex_top" file="complex.top" ftype="top" compare="diff" lines_diff="20"/>
35 <output name="complex_gro" file="complex.gro" ftype="gro"/>
27 </test> 36 </test>
28 </tests> 37 </tests>
29 <help><![CDATA[ 38 <help><![CDATA[
30 39
31 .. class:: infomark 40 .. class:: infomark
32 41
33 **What it does** 42 **What it does**
34 43
35 This tool merges GROMACS topologies - for example, the topology files for a ligand and protein. TOP files contain references to other subordinate TOP files using the `#include` tag. In Galaxy, these tags need to be replaced directly with the contents of the topology files they refer to. 44 This tool merges GROMACS topologies and structure (GRO) files, calculated separately for a protein and ligand, into combined topology and GRO files for the resulting complex.
45
46 The tool will work best if used with the outputs of the 'acpype' and 'GROMACS initial setup' tools. If the input files are formatted unusually or incorrectly, it will probably fail.
36 47
37 _____ 48 _____
38 49
39 .. class:: infomark 50 .. class:: infomark
40 51
41 **Input** 52 **Input**
42 53
43 - TOP file for the main topology 54 - TOP file for the protein topology
44 - One or more subordinate topologies (TOP or ITP) which can be inserted into the main topology if specified by an `#include` tag. 55 - A TOP or ITP file for the ligand topology
56 - GRO file for the protein structure
57 - GRO file for the ligand structure
45 58
46 _____ 59 _____
47 60
48 61
49 .. class:: infomark 62 .. class:: infomark
50 63
51 **Output** 64 **Output**
52 65
53 - TOP file. 66 - TOP file for the protein-ligand complex.
67 - GRO file for the protein-ligand complex.
54 68
55 ]]></help> 69 ]]></help>
56 <expand macro="citations" /> 70 <citations>
71 <citation type="bibtex">
72 @misc{parmed_2020,
73 author = {Jason Swails and other contributors},
74 title = {ParmEd},
75 url={https://github.com/ParmEd/ParmEd},
76 abstract = {Parameter/topology editor and molecular simulator.},
77 urldate = {2020-04-03},
78 publisher = {GitHub},
79 year = {2020},
80 month = mar, }</citation>
81 </citations>
57 </tool> 82 </tool>