diff minim.xml @ 4:c1e98d48b8b4 draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"

--- a/minim.xml	Fri Aug 30 15:04:13 2019 -0400
+++ b/minim.xml	Mon Oct 07 12:48:06 2019 -0400
@@ -47,8 +47,6 @@
     <inputs>
         <param argument="gro_input" type="data" format='gro' label="GRO structure file."/>
         <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/>
-        <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/>
-
         <conditional name="mdp">
             <param name="mdpfile" type="select" label="Parameter input">
                 <option value="custom">Upload own MDP file</option>
@@ -81,6 +79,7 @@
                 <param argument="emstep" type="float" label="Maximum step size /nm" value="0.01" min="0.0001" max="1.0" help="Initial step size in nm." />
             </when>
         </conditional>
+        <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
     </inputs>
     <outputs>
         <data name="output1" format="gro" from_work_dir="em.gro"/>
@@ -115,7 +114,34 @@
     </tests>
     <help><![CDATA[
 
-Upload GRO and TOP files for energy minimisation. To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html for more information on the options.
+.. class:: infomark
+
+**What it does**
+
+This tool performs energy minimization of a system prior to a GROMACS simulation.
+
+_____
+
+.. class:: infomark
+
+**Input**
+
+       - GRO structure file.
+       - Topology (TOP) file.
+       - MDP parameter file (optional)
+
+To take advantage of all GROMACS features, upload an MDP file with simulation parameters. Otherwise, choose parameters through the Galaxy interface. See the `manual`_ for more information on the options.
+
+.. _`manual`: http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html
+
+_____
+
+        
+.. class:: infomark
+
+**Output**
+
+       - GRO structure file.
 
     ]]></help>