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Commit message:
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975" |
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modified:
macros.xml sim.xml |
| b |
| diff -r da8753545526 -r 525ca7c8065f macros.xml --- a/macros.xml Wed Sep 29 07:40:59 2021 +0000 +++ b/macros.xml Wed Oct 27 08:02:22 2021 +0000 |
| b |
| @@ -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 da8753545526 -r 525ca7c8065f sim.xml --- a/sim.xml Wed Sep 29 07:40:59 2021 +0000 +++ b/sim.xml Wed Oct 27 08:02:22 2021 +0000 |
| [ |
| @@ -2,7 +2,7 @@ <description>for system equilibration or data collection</description> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">1</token> + <token name="@GALAXY_VERSION@">2</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -41,7 +41,7 @@ -n ./index.ndx #end if -p ./top_input.top - -o outp.tpr &>> verbose.txt && + -o outp.tpr @MAXWARN_CMD@ &>> verbose.txt && #if "\${GPU_AVAILABLE:-0}" == 1: gmx_gpu mdrun @@ -229,7 +229,8 @@ <expand macro="md_inputs"/> </section> - + + <expand macro="maxwarn" /> <expand macro="log" /> </inputs> |