Mercurial > repos > fmercuri > gmx_merge_files_daimoners
changeset 0:2f5e955d7ea5 draft
Uploaded
author | fmercuri |
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date | Fri, 25 Jun 2021 17:55:42 +0000 |
parents | |
children | 917bea0e779d |
files | merge_top.xml |
diffstat | 1 files changed, 70 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/merge_top.xml Fri Jun 25 17:55:42 2021 +0000 @@ -0,0 +1,70 @@ +<tool id="gmx_merge_files_daimoners" name="Merge GROMACS topologies daimoners version" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>and GRO files</description> + <macros> + <token name="@TOOL_VERSION@">3.2.0</token> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">parmed</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + cat $main_top $mol_top $itp_file > complete.top + ]]></command> + <inputs> + <param name="main_top" type="data" format='top' label="Main topology (TOP) file" help="Main topology file."/> + <param name="mol_top" type="data" format='top,itp' label="Molecule topology (TOP or ITP) file" help="Molecule topology file. Either TOP or ITP format."/> + <param name="itp_file" type="data" format='itp' label="Force field (ITP) file" help="Force field ITP file."/> + </inputs> + <outputs> + <data name="complete_top" format="top" from_work_dir="complete.top"/> + </outputs> + <tests> + <test> + <param name="prot_top" value="topol.top" /> + <param name="lig_top" value="lig.itp" /> + <param name="prot_gro" value="newbox.gro" /> + <param name="lig_gro" value="lig.gro" /> + <output name="complex_top" file="complex.top" ftype="top" compare="diff" lines_diff="20"/> + <output name="complex_gro" file="complex.gro" ftype="gro"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +This tool merges topology and force-field GROMACS files. + +_____ + +.. class:: infomark + +**Input** + + - TOP file for the description of the system. + - A TOP or ITP file for the molecular topology. + - A ITP force-field file. +_____ + + +.. class:: infomark + +**Output** + + - TOP overall file. + + ]]></help> + <citations> + <citation type="bibtex"> +@misc{parmed_2020, +author = {Jason Swails and other contributors}, +title = {ParmEd}, +url={https://github.com/ParmEd/ParmEd}, +abstract = {Parameter/topology editor and molecular simulator.}, +urldate = {2020-04-03}, +publisher = {GitHub}, +year = {2020}, +month = mar, }</citation> + </citations> +</tool>