Previous changeset 14:d532b7e5f64b (2021-09-29) Next changeset 16:bfca1eee5aa2 (2021-11-30) |
Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975" |
modified:
macros.xml minim.xml |
b |
diff -r d532b7e5f64b -r 59c662ca4211 macros.xml --- a/macros.xml Wed Sep 29 07:43:54 2021 +0000 +++ b/macros.xml Wed Oct 27 07:59:52 2021 +0000 |
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@@ -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 ${on_string}"> <filter>capture_log</filter> |
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diff -r d532b7e5f64b -r 59c662ca4211 minim.xml --- a/minim.xml Wed Sep 29 07:43:54 2021 +0000 +++ b/minim.xml Wed Oct 27 07:59:52 2021 +0000 |
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@@ -2,7 +2,7 @@ <description>of the system prior to equilibration and production MD</description> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> <expand macro="requirements" /> @@ -18,7 +18,7 @@ ln -s '$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> |