--- a/solvate.xml	Fri May 08 07:31:18 2020 -0400
+++ b/solvate.xml	Wed May 20 12:57:49 2020 -0400
@@ -1,7 +1,8 @@
-<tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@VERSION@">
+<tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
     <description>to structure and topology files</description>
     <macros>
         <import>macros.xml</import>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
 
     <expand macro="requirements" />
@@ -17,7 +18,7 @@
         #if $neutralise == "true":
             &&
             gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt &&
-            echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt &&
+            echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral -conc $conc &>> verbose.txt &&
             mv solv_ions.gro solv.gro
         #end if
 
@@ -26,7 +27,8 @@
         <configfiles>
             <!-- .mdp file for the gromacs simulation -->
             <configfile name="ions">
-: Parameters are not so important here as no simulation is run
+
+; Parameters are not so important here as no simulation is run
 integrator  = steep
 emtol    = 1000.0
 emstep      = 0.01 
@@ -53,6 +55,8 @@
             <option value="false">No</option>
         </param>
 
+        <param argument="conc" type="float" value="0" min="0" max="6" label="Specify salt concentration (sodium chloride) to add, in mol/liter" help="Note existing ions in the system are not taken into account - including those added if the neutralise option is selected. Ions are added by randomly replacing water molecules." />
+
         <expand macro="log" />
 
     </inputs>
@@ -67,22 +71,39 @@
             <param name="neutralise" value="true" />
             <param name="top_input" value="topol.top" />
             <param name="water_model" value="spc216" />
+            <param name="conc" value="1" />
             <output name="output1" ftype="gro">
                 <!-- replacement of water with ions is random, thus we cannot compare the whole file -->
                 <assert_contents>
-                    <has_text text="1.014   5.822   2.833"/>
-                    <has_text text="6.831   5.961   6.119"/>
-                    <has_text text="3.592   6.520   5.241"/>
+                    <has_text text="1.671   1.591   3.533"/>
+                    <has_text text="2.032   2.417   1.345"/>
+                    <has_text text="3.438   1.662   0.307"/>
+                    <has_text text="2218CL"/>
+                    <has_text text="2147NA"/>
                 </assert_contents>
             </output>
-            <output name="output2" file="topol_solv.top" ftype="top"/>
+            <output name="output2" file="topol_solv.top" ftype="top" lines_diff="4">
+                <assert_contents>
+                    <has_line line="SOL         2130" />
+                    <has_line line="NA               41" />
+                    <has_line line="CL               43" />
+                </assert_contents>
+            </output>
         </test>
         <test>
             <param name="gro_input" value="newbox.gro" />
             <param name="neutralise" value="false" />
-            <param name="top_input" value="topol.top" />
+            <param name="top_input" value="topol.top"/>
             <param name="water_model" value="spc216" />
-            <output name="output1" file="solv.gro" ftype="gro"/>
+            <param name="conc" value="0" />
+            <output name="output1" ftype="gro">
+                <assert_contents>
+                    <has_text text="1.671   1.591   3.533"/>
+                    <has_text text="2.032   2.417   1.345"/>
+                    <has_text text="3.438   1.662   0.307"/>
+                    <not_has_text text="2218CL"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
@@ -91,7 +112,7 @@
 
 **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.
+This tool solvates a system prior to a GROMACS simulation. In addition, sodium or chloride ions can be added if necessary to ensure the system is charge-neutral.
 
 _____