diff solvate.xml @ 3:7161b230adad draft

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

--- a/solvate.xml	Fri Aug 30 15:03:34 2019 -0400
+++ b/solvate.xml	Mon Oct 07 12:47:31 2019 -0400
@@ -37,14 +37,14 @@
             </configfile>
         </configfiles>
     <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="water_model" type="select"  label="Water model for solvation.">
+        <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="water_model" type="select"  label="Water model for solvation">
             <option value="tip3p">TIP3P</option>
             <option value="tip4p">TIP4P</option>
             <option value="spc216">SPC</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."/>
 
     </inputs>
     <outputs>
@@ -65,7 +65,31 @@
     </tests>
     <help><![CDATA[
 
-Select a water model - consistent with the one selected in system set-up and provide GRO and TOP files to be updated with the added water molecules. In addition, sodium or chloride ions are added if necessary to ensure the system is charge-neutral.
+.. class:: infomark
+
+**What it does**
+
+This tool solvates a system prior to a GROMACS simulation. In addition, sodium or chloride ions will be added if necessary to ensure the system is charge-neutral.
+
+_____
+
+.. class:: infomark
+
+**Input**
+
+       - GRO structure file.
+       - Topology (TOP) file.
+
+In addition, a water model must be selected - this should be consistent with the one selected previously in the system setup.
+
+_____
+
+        
+.. class:: infomark
+
+**Output**
+
+       - GRO structure file.
 
     ]]></help>