# HG changeset patch
# User chemteam
# Date 1603190619 0
# Node ID e205c82e99592b0bba82fb61e2a173c8e39b6244
# Parent  27ea4e1a3f95b51332371477a74d83529654d8c4
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"

diff -r 27ea4e1a3f95 -r e205c82e9959 solvate.xml
--- a/solvate.xml	Wed May 20 12:57:49 2020 -0400
+++ b/solvate.xml	Tue Oct 20 10:43:39 2020 +0000
@@ -2,7 +2,7 @@
     <description>to structure and topology files</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">0</token>
+        <token name="@GALAXY_VERSION@">1</token>
     </macros>
 
     <expand macro="requirements" />
@@ -13,16 +13,14 @@
         ln -s '$gro_input' ./gro_input.gro &&
         ln -s '$top_input' ./top_input.top &&
 
-        gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt
-
-        #if $neutralise == "true":
+        gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt &&
+        gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt
+        #if $neutralise and $conc:  ## else this step would do nothing
             &&
-            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 -conc $conc &>> verbose.txt &&
+            echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL $neutralise -conc $conc &>> verbose.txt &&
             mv solv_ions.gro solv.gro
         #end if
 
-
     ]]></command>
         <configfiles>
             <!-- .mdp file for the gromacs simulation -->
@@ -51,8 +49,8 @@
             <option value="tip5p">TIP5P (five-point model)</option>
         </param>
         <param name="neutralise" label="Add ions to neutralise system?" type="select" help="If system is charged, replace an appropriate number of randomly selected solvent molecules with sodium or chloride ions to neutralise it.">
-            <option value="true">Yes, add ions</option>
-            <option value="false">No</option>
+            <option value="-neutral">Yes, add ions</option>
+            <option value="">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." />
@@ -68,7 +66,7 @@
     <tests>
         <test>
             <param name="gro_input" value="newbox.gro" />
-            <param name="neutralise" value="true" />
+            <param name="neutralise" value="-neutral" />
             <param name="top_input" value="topol.top" />
             <param name="water_model" value="spc216" />
             <param name="conc" value="1" />
@@ -92,7 +90,7 @@
         </test>
         <test>
             <param name="gro_input" value="newbox.gro" />
-            <param name="neutralise" value="false" />
+            <param name="neutralise" value="" />
             <param name="top_input" value="topol.top"/>
             <param name="water_model" value="spc216" />
             <param name="conc" value="0" />