Mercurial > repos > chemteam > gmx_sim
comparison sim.xml @ 14:525ca7c8065f draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit bf18581ac3de6b65bdc0a988e6f844cea6e77975"
| author | chemteam |
|---|---|
| date | Wed, 27 Oct 2021 08:02:22 +0000 |
| parents | da8753545526 |
| children | ea0e6d2f1be7 |
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| 13:da8753545526 | 14:525ca7c8065f |
|---|---|
| 1 <tool id="gmx_sim" name="GROMACS simulation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | 1 <tool id="gmx_sim" name="GROMACS simulation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> |
| 2 <description>for system equilibration or data collection</description> | 2 <description>for system equilibration or data collection</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 <token name="@GALAXY_VERSION@">1</token> | 5 <token name="@GALAXY_VERSION@">2</token> |
| 6 </macros> | 6 </macros> |
| 7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
| 8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
| 9 #if $sets.mdp.mdpfile == "custom": | 9 #if $sets.mdp.mdpfile == "custom": |
| 10 ln -s '$sets.mdp.mdp_input' ./md.mdp && | 10 ln -s '$sets.mdp.mdp_input' ./md.mdp && |
| 39 #end if | 39 #end if |
| 40 #if $inps.ndx_in: | 40 #if $inps.ndx_in: |
| 41 -n ./index.ndx | 41 -n ./index.ndx |
| 42 #end if | 42 #end if |
| 43 -p ./top_input.top | 43 -p ./top_input.top |
| 44 -o outp.tpr &>> verbose.txt && | 44 -o outp.tpr @MAXWARN_CMD@ &>> verbose.txt && |
| 45 | 45 |
| 46 #if "\${GPU_AVAILABLE:-0}" == 1: | 46 #if "\${GPU_AVAILABLE:-0}" == 1: |
| 47 gmx_gpu mdrun | 47 gmx_gpu mdrun |
| 48 -ntmpi 1 | 48 -ntmpi 1 |
| 49 -nb gpu | 49 -nb gpu |
| 227 <option value="npt">Isothermal-isobaric ensemble (NPT)</option> | 227 <option value="npt">Isothermal-isobaric ensemble (NPT)</option> |
| 228 </param> | 228 </param> |
| 229 | 229 |
| 230 <expand macro="md_inputs"/> | 230 <expand macro="md_inputs"/> |
| 231 </section> | 231 </section> |
| 232 | 232 |
| 233 <expand macro="maxwarn" /> | |
| 233 <expand macro="log" /> | 234 <expand macro="log" /> |
| 234 | 235 |
| 235 </inputs> | 236 </inputs> |
| 236 <outputs> | 237 <outputs> |
| 237 <data name="output1" format="gro" from_work_dir="outp.gro" label="GROMACS simulation (GRO) on ${on_string}"> | 238 <data name="output1" format="gro" from_work_dir="outp.gro" label="GROMACS simulation (GRO) on ${on_string}"> |