# HG changeset patch
# User chemteam
# Date 1570466966 14400
# Node ID f2faba46d68058651d3ae1dda66d106b06506d71
# Parent  9987b0933704b2c73972ee8712879d5d65eb7e45
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"

diff -r 9987b0933704 -r f2faba46d680 macros.xml
--- a/macros.xml	Fri Aug 30 15:06:06 2019 -0400
+++ b/macros.xml	Mon Oct 07 12:49:26 2019 -0400
@@ -1,8 +1,8 @@
 <macros>
-    <token name="@VERSION@">2019.1</token>
+    <token name="@VERSION@">2019.1.1</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">gromacs</requirement>
+            <requirement type="package" version="2019.1">gromacs</requirement>
         </requirements>
     </xml>
     <xml name="citations">
@@ -11,32 +11,46 @@
         </citations>
     </xml>
     <xml name="md_inputs">
+        <param argument="traj" type="select" label="Trajectory output">
+            <option value='none'>Return no trajectory output</option>
+            <option value='xtc'>Return .xtc file (reduced precision)</option>
+            <option value='trr'>Return .trr file (full precision)</option>
+            <option value='both'>Return both .xtc and .trr files</option>
+        </param>
+
+        <param argument="str" type="select" label="Structure output">
+            <option value='none'>Return no structure output</option>
+            <option value='gro'>Return .gro file</option>
+            <option value='pdb'>Return .pdb file</option>
+            <option value='both'>Return both .gro and .pdb files</option>
+        </param>
+
         <conditional name="mdp">
             <param name="mdpfile" type="select" label="Parameter input">
                 <option value="custom">Upload own MDP file</option>
                 <option value="default">Use default (partially customisable) setting</option>
             </param>
             <when value="custom">
-                <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)."/>
+                <param argument="mdp_input" type="data" format='mdp' label="MD parameters (MDP) file (optional; default settings if not set)"/>
             </when>
             <when value="default">
-                <param argument="integrator" type="select" label="Choice of integrator.">
+                <param argument="integrator" type="select" label="Choice of integrator">
                     <option value="md">A leap-frog algorithm for integrating Newton's equations of motion.</option>
                     <option value="sd">Stochastic dynamics integrator</option>
                     <option value="bd">An Euler integrator for Brownian or position Langevin dynamics.</option>
                 </param>
-                <param argument="constraints" type="select" label="Bond constraints (constraints).">
+                <param argument="constraints" type="select" label="Bond constraints (constraints)">
                     <option value="none">No constraints except for those defined explicitly in the topology (none).</option>
                     <option value="h-bonds">Bonds with H-atoms. (h-bonds).</option>
                     <option value="all-bonds">All bonds (all-bonds).</option>
                     <option value="h-angles">Bonds and angles with H-atoms. (h-angles).</option>
                     <option value="all-angles">All bonds and angles (all-angles).</option>
                 </param>
-                <param argument="cutoffscheme" type="select" label="Neighbor searching.">
+                <param argument="cutoffscheme" type="select" label="Neighbor searching">
                     <option value="Verlet">Generate a pair list with buffering.</option>
                     <option value="group">Generate a pair list for groups of atoms.</option>
                 </param>
-                <param argument="coulombtype" type="select" label="Electrostatics.">
+                <param argument="coulombtype" type="select" label="Electrostatics">
                     <option value="PME">Fast smooth Particle-Mesh Ewald (SPME) electrostatics.</option>
                     <option value="P3M-AD">Particle-Particle Particle-Mesh algorithm with analytical derivative.</option>
                     <option value="Reaction-Field-zero">Reaction field electrostatics.</option>
@@ -48,27 +62,13 @@
                 <param argument="rcoulomb" value="1.0" type="float" label="Distance for the Coulomb cut-off."/>
                 <param argument="rlist" value="1.0" type="float" label="Cut-off distance for the short-range neighbor list. Ignored if the Verlet cutoff scheme is set."/>
                 <param argument="rvdw" value="1.0" type="float" label="Short range van der Waals cutoff."/>
-                <param argument="md_steps" type="integer" label="Number of steps for the NPT equilibration" value="0" min="0" max="1000000" help="NPT steps" />
+                <param argument="md_steps" type="integer" label="Number of steps for the simulation" value="0" min="0" max="1000000" help="NPT steps" />
                 
             </when>
 
         </conditional>
-        
-        <param argument="traj" type="select" label="Trajectory output.">
-            <option value='none'>Return no trajectory output</option>
-            <option value='xtc'>Return .xtc file (reduced precision)</option>
-            <option value='trr'>Return .trr file (full precision)</option>
-            <option value='both'>Return both .xtc and .trr files</option>
-        </param>
 
-        <param argument="str" type="select" label="Structure output.">
-            <option value='none'>Return no trajectory output</option>
-            <option value='gro'>Return .gro file</option>
-            <option value='pdb'>Return .pdb file</option>
-            <option value='both'>Return both .gro and .pdb files</option>
-        </param>
-
-        <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
+        <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
 
 
     </xml>
diff -r 9987b0933704 -r f2faba46d680 merge_top.xml
--- a/merge_top.xml	Fri Aug 30 15:06:06 2019 -0400
+++ b/merge_top.xml	Mon Oct 07 12:49:26 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="0.1.0">
+<tool id="gmx_merge_topology_files" name="Merge GROMACS topologies" version="@VERSION@">
     <description>for example, for protein and ligand files</description>
     <macros>
         <import>macros.xml</import>
@@ -13,8 +13,8 @@
         python '$__tool_directory__/merge_top.py' top_input.top itps.txt
     ]]></command>
     <inputs>
-        <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
-        <param argument="itp_inputs" type="data" format='itp' multiple="true" label="Position restraint file"/>
+        <param name="top_input" type="data" format='top' label="Topology (TOP) file" help="'Master' topology into which subordinate topologies will be added."/>
+        <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."/>
     </inputs>
     <outputs>
         <data name="output" format="top" from_work_dir="top_output.top"/>
@@ -27,7 +27,31 @@
         </test>
     </tests>
     <help><![CDATA[
-        Use this tool to combine GROMACS topologies - for example, the topology files for a ligand and protein.
+
+.. class:: infomark
+
+**What it does**
+
+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.
+
+_____
+
+.. class:: infomark
+
+**Input**
+
+       - TOP file for the main topology
+       - One or more subordinate topologies (TOP or ITP) which can be inserted into the main topology if specified by an `#include` tag.
+
+_____
+
+        
+.. class:: infomark
+
+**Output**
+
+       - TOP file.
+
     ]]></help>
     <expand macro="citations" />
 </tool>