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comparison sim.xml @ 14:525ca7c8065f 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 08:02:22 +0000
parents da8753545526
children ea0e6d2f1be7
comparison
equal deleted inserted replaced
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}">