Mercurial > repos > recetox > qcxms_neutral_run
changeset 5:33b7a99b6de3 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/qcxms commit 5a088c3d758c9a1dbd119dad55ecffa173139a40
| author | recetox |
|---|---|
| date | Thu, 17 Oct 2024 06:17:48 +0000 |
| parents | 8f465c0c3b6c |
| children | 475bbef634d4 |
| files | qcxms_neutral_run.xml test-data/TMP.1_qcxms_in.txt |
| diffstat | 2 files changed, 10 insertions(+), 5 deletions(-) [+] |
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--- a/qcxms_neutral_run.xml Thu Jul 25 14:27:01 2024 +0000 +++ b/qcxms_neutral_run.xml Thu Oct 17 06:17:48 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy4" profile="22.09"> +<tool id="qcxms_neutral_run" name="QCxMS neutral run" version="@TOOL_VERSION@+galaxy5" profile="22.09"> <description>required as first step to prepare for the production runs</description> <macros> @@ -30,7 +30,9 @@ #end if tmax ${keywords.tmax} tinit ${keywords.tinit} -ieeatm ${keywords.ieeatm}]]> +ieeatm ${keywords.ieeatm} +tstep ${keywords.tstep} +etemp ${keywords.etemp}]]> </configfile> <configfile filename="rename.py"> import os @@ -64,11 +66,12 @@ <section name="keywords" title="Advanced method parameters" expanded="false" help="List of advanced keywords to specify the method - for more information see [1]."> <param name="tmax" type="float" value="20.0" label="Maximum MD time (sampling) [ps]" - help="MD time for the mean-free-path (mfp) simulation in the EI mode. In the CID mode, this sets the number of time steps for the simulation - after fragmentation during internal energy scaling (implicit run type). For the explicit run type, the time for the collision MDs is fixed at 50 fs * number_of_atoms."/> + help="MD time for the mean-free-path (mfp) simulation in the EI mode."/> <param name="tinit" type="float" value="500.0" label="Initial Temperature [K]"/> <param name="ieeatm" type="float" value="0.6" label="Impact excess energy (IEE) per atom [eV/atom]" /> <param name="ntraj" type="integer" optional="true" min="2" label="Number of trajectories[#]" help="Default is 25 * no. of atoms if unspecified."/> + <param name="tstep" type="float" value="0.5" label="MD time step (tstep) [fs]" help="Default is 0.5 fs."/> + <param name="etemp" type="float" value="5000" label="Electronic temperature (etemp) [K]" help="Default is 5000 K."/> </section> <param name="store_extended_output" type="boolean" value="false" label="Store additional outputs?" help="Output the logfile and generated trajectory."/> </inputs> @@ -117,7 +120,7 @@ </output> <output name="log"> <assert_contents> - <has_size value="10518" delta="300"/> + <has_size value="10518" delta="500"/> </assert_contents> </output> </test>