diff minim.xml @ 14:d532b7e5f64b draft

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 2f3d14b4f200100881e362b0f3b97f0e8a36d1f3"

--- a/minim.xml	Mon Nov 23 10:47:01 2020 +0000
+++ b/minim.xml	Wed Sep 29 07:43:54 2021 +0000
@@ -31,6 +31,7 @@
                     emtol    = $mdp.emtol     ; Stop minimization when the maximum force is less than this value
                     emstep      = $mdp.emstep      ; Energy step size
                     nsteps    = $mdp.md_steps      ; Maximum number of (minimization) steps to perform
+                    gen-seed  = $mdp.seed              ; random seed
 
                     ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
                     nstlist        = 1        ; Frequency to update the neighbor list and long range forces
@@ -78,19 +79,20 @@
                 <param argument="md_steps" type="integer" label="Number of steps for the MD simulation" value="0" min="0" max="1000000" help="MD steps" />
                 <param argument="emtol" type="float" label="EM tolerance" value="0" min="0" max="10000" help="The minimization is converged when the maximum force is smaller than this value" />
                 <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." />
+                <param argument="seed" type="integer" label="Random seed" value="1" min="-1" help="Select a random seed for initial velocity generation. Set to -1 to generate a seed." />
             </when>
         </conditional>
         <expand macro="log" />
     </inputs>
     <outputs>
-        <data name="output1" format="gro" from_work_dir="em.gro"/>
-        <data name="output2" format="edr" from_work_dir="em.edr"/>
+        <data name="output1" format="gro" from_work_dir="em.gro" label="GROMACS energy minimization (GRO) on ${on_string}"/>
+        <data name="output2" format="edr" from_work_dir="em.edr" label="GROMACS energy minimization (EDR) on ${on_string}"/>
         <expand macro="log_outputs" />
     </outputs>
     <tests>
         <test>
             <param name="gro_input" value="str_ions.gro" />
-            <param name="top_input" value="topol_solv.top" />
+            <param name="top_input" value="topol_md.top" />
             <param name="mdpfile" value="default" />
             <param name="integrator" value="steep" />
             <param name="cutoffscheme" value="Verlet" />
@@ -100,32 +102,22 @@
             <param name="md_steps" value="50000" />
             <param name="emtol" value="1000.0" />
             <param name="emstep" value="0.01" />
-            <output name="output1" ftype="gro" >
-                <assert_contents>
-                    <has_size value="4281" />
-                </assert_contents>
-            </output>
+            <output name="output1" file="minim.gro" ftype="gro" lines_diff="20" />
             <output name="output2" ftype="edr" >
                 <assert_contents>
-                    <!-- this binary can vary in size a lot unfortunately -->
-                    <has_size value="5000" delta="1000" />
+                    <has_size value="5644"/>
                 </assert_contents>
             </output>
         </test>
         <test>
             <param name="gro_input" value="str_ions.gro" />
-            <param name="top_input" value="topol_solv.top" />
+            <param name="top_input" value="topol_md.top" />
             <param name="mdpfile" value="custom" />
             <param name="mdp_input" value="minim.mdp" />
-            <output name="output1" ftype="gro" >
-                <assert_contents>
-                    <has_size value="4281" />
-                </assert_contents>
-            </output>
+            <output name="output1" file="minim.gro" ftype="gro" lines_diff="20" />
             <output name="output2" ftype="edr" >
                 <assert_contents>
-                    <!-- this binary can vary in size a lot unfortunately -->
-                    <has_size value="5000" delta="1000" />
+                    <has_size value="5644"/>
                 </assert_contents>
             </output>
         </test>