Mercurial > repos > chemteam > gmx_merge_topology_files

comparison merge_top.xml @ 2:f2faba46d680 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:49:26 -0400
parents 33ed3c26b8c2
children 06ea4e040d45
comparison
equal deleted inserted replaced
1:9987b0933704 2:f2faba46d680
1 <tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="0.1.0"> 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>for example, for protein and ligand files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
11 #end for 11 #end for
12 12
13 python '$__tool_directory__/merge_top.py' top_input.top itps.txt 13 python '$__tool_directory__/merge_top.py' top_input.top itps.txt
14 ]]></command> 14 ]]></command>
15 <inputs> 15 <inputs>
16 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/> 16 <param name="top_input" type="data" format='top' label="Topology (TOP) file" help="'Master' topology into which subordinate topologies will be added."/>
17 <param argument="itp_inputs" type="data" format='itp' multiple="true" label="Position restraint file"/> 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."/>
18 </inputs> 18 </inputs>
19 <outputs> 19 <outputs>
20 <data name="output" format="top" from_work_dir="top_output.top"/> 20 <data name="output" format="top" from_work_dir="top_output.top"/>
21 </outputs> 21 </outputs>
22 <tests> 22 <tests>
25 <param name="itp_inputs" value="posres.itp" /> 25 <param name="itp_inputs" value="posres.itp" />
26 <output name="output" file="top_output.top" ftype="top" /> 26 <output name="output" file="top_output.top" ftype="top" />
27 </test> 27 </test>
28 </tests> 28 </tests>
29 <help><![CDATA[ 29 <help><![CDATA[
30 Use this tool to combine GROMACS topologies - for example, the topology files for a ligand and protein. 30
31 .. class:: infomark
32
33 **What it does**
34
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.
36
37 _____
38
39 .. class:: infomark
40
41 **Input**
42
43 - TOP file for the main topology
44 - One or more subordinate topologies (TOP or ITP) which can be inserted into the main topology if specified by an `#include` tag.
45
46 _____
47
48
49 .. class:: infomark
50
51 **Output**
52
53 - TOP file.
54
31 ]]></help> 55 ]]></help>
32 <expand macro="citations" /> 56 <expand macro="citations" />
33 </tool> 57 </tool>