Mercurial > repos > chemteam > gmx_em

changeset 15:59c662ca4211 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975"
author chemteam
date Wed, 27 Oct 2021 07:59:52 +0000
parents d532b7e5f64b
children bfca1eee5aa2
files macros.xml minim.xml
diffstat 2 files changed, 10 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Wed Sep 29 07:43:54 2021 +0000
+++ b/macros.xml	Wed Oct 27 07:59:52 2021 +0000
@@ -5,6 +5,9 @@
             <requirement type="package" version="@TOOL_VERSION@">gromacs</requirement>
         </requirements>
     </xml>
+
+    <token name="@MAXWARN_CMD@">-maxwarn '$mxw'</token>
+
     <xml name="citations">
         <citations>
             <citation type="doi">10.1016/j.softx.2015.06.001</citation>
@@ -61,6 +64,10 @@
         <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
     </xml>
 
+    <xml name="maxwarn">
+        <param name="mxw" value="0" min="0" argument="-maxwarn" type="integer" label="Maximum warnings to allow." help="Do not use this unless you know what you are doing. This option allows you to override non-fatal warnings, that would otherwise cause the simulation to fail."/>
+    </xml>
+
     <xml name="log_outputs">
         <data name="report" format="txt" from_work_dir="verbose.txt" label="GROMACS log file on ${on_string}">
             <filter>capture_log</filter>
--- a/minim.xml	Wed Sep 29 07:43:54 2021 +0000
+++ b/minim.xml	Wed Oct 27 07:59:52 2021 +0000
@@ -2,7 +2,7 @@
     <description>of the system prior to equilibration and production MD</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">0</token>
+        <token name="@GALAXY_VERSION@">1</token>
     </macros>
 
     <expand macro="requirements" />
@@ -18,7 +18,7 @@
         ln -s '$gro_input' ./solv_ions.gro &&
         ln -s '$top_input' ./top_input.top &&
   
-        gmx grompp -f ./minim.mdp -c ./solv_ions.gro -r ./solv_ions.gro -p ./top_input.top -o em.tpr &>> verbose.txt &&
+        gmx grompp -f ./minim.mdp -c ./solv_ions.gro -r ./solv_ions.gro -p ./top_input.top -o em.tpr @MAXWARN_CMD@ &>> verbose.txt &&
         gmx mdrun -nt "\${GALAXY_SLOTS:-4}" -deffnm em &>> verbose.txt
         
     ]]></command>
@@ -82,6 +82,7 @@
                 <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="maxwarn" />
         <expand macro="log" />
     </inputs>
     <outputs>