# HG changeset patch
# User fmercuri
# Date 1624644181 0
# Node ID 579c8f2d27e80998fea2275cec139071477d3f89
# Parent  917bea0e779d8ee71536494f627fd4cc64057b53
Uploaded

diff -r 917bea0e779d -r 579c8f2d27e8 merge_top.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_top.xml	Fri Jun 25 18:03:01 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 $itp_file $mol_top $main_top > 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>