# HG changeset patch
# User chemteam
# Date 1636396842 0
# Node ID 9a1e472aa5159d16d72b55e5c4ff38423a561d1f
# Parent  61094e01eff9d4ad17510515e09860cdd8dc0bae
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 04ccbbe525c43164b061fe738500a84d73f89afa"

diff -r 61094e01eff9 -r 9a1e472aa515 solvate.xml
--- a/solvate.xml	Wed Oct 27 08:00:42 2021 +0000
+++ b/solvate.xml	Mon Nov 08 18:40:42 2021 +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" />
@@ -14,7 +14,7 @@
         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 &&
-        gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt
+        gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr @MAXWARN_CMD@ &>> verbose.txt
         #if $neutralise or $conc:  ## else this step would do nothing
             &&
             echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL $neutralise -conc $conc -seed $seed &>> verbose.txt &&
@@ -56,6 +56,7 @@
         <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." />
         <param argument="seed" type="integer" value="1" min="0" label="Random seed for adding ions" help="Select a random seed for replacing solvent with ions. Set to 0 to generate a seed." />
 
+        <expand macro="maxwarn" />
         <expand macro="log" />
 
     </inputs>