Mercurial > repos > chemteam > gmx_em
comparison minim.xml @ 12:55918daa5651 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
| author | chemteam |
|---|---|
| date | Wed, 20 May 2020 12:58:59 -0400 |
| parents | dc98e5c8165a |
| children | d532b7e5f64b |
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| 11:dc98e5c8165a | 12:55918daa5651 |
|---|---|
| 1 <tool id="gmx_em" name="GROMACS energy minimization" version="@VERSION@"> | 1 <tool id="gmx_em" name="GROMACS energy minimization" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> |
| 2 <description>of the system prior to equilibration and production MD</description> | 2 <description>of the system prior to equilibration and production MD</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 <token name="@GALAXY_VERSION@">0</token> | |
| 5 </macros> | 6 </macros> |
| 6 | 7 |
| 7 <expand macro="requirements" /> | 8 <expand macro="requirements" /> |
| 8 | 9 |
| 9 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
| 86 <data name="output2" format="edr" from_work_dir="em.edr"/> | 87 <data name="output2" format="edr" from_work_dir="em.edr"/> |
| 87 <expand macro="log_outputs" /> | 88 <expand macro="log_outputs" /> |
| 88 </outputs> | 89 </outputs> |
| 89 <tests> | 90 <tests> |
| 90 <test> | 91 <test> |
| 91 <param name="gro_input" value="solv_ions.gro" /> | 92 <param name="gro_input" value="str_ions.gro" /> |
| 92 <param name="top_input" value="topol_solv.top" /> | 93 <param name="top_input" value="topol_solv.top" /> |
| 93 <param name="mdpfile" value="default" /> | 94 <param name="mdpfile" value="default" /> |
| 94 <param name="integrator" value="steep" /> | 95 <param name="integrator" value="steep" /> |
| 95 <param name="cutoffscheme" value="Verlet" /> | 96 <param name="cutoffscheme" value="Verlet" /> |
| 96 <param name="coulombtype" value="PME" /> | 97 <param name="coulombtype" value="PME" /> |
| 99 <param name="md_steps" value="50000" /> | 100 <param name="md_steps" value="50000" /> |
| 100 <param name="emtol" value="1000.0" /> | 101 <param name="emtol" value="1000.0" /> |
| 101 <param name="emstep" value="0.01" /> | 102 <param name="emstep" value="0.01" /> |
| 102 <output name="output1" ftype="gro" > | 103 <output name="output1" ftype="gro" > |
| 103 <assert_contents> | 104 <assert_contents> |
| 104 <has_size value="1726975" /> | 105 <has_size value="4281" /> |
| 105 </assert_contents> | 106 </assert_contents> |
| 106 </output> | 107 </output> |
| 107 <output name="output2" ftype="edr" > | 108 <output name="output2" ftype="edr" > |
| 108 <assert_contents> | 109 <assert_contents> |
| 109 <!-- this binary can vary in size a lot unfortunately --> | 110 <!-- this binary can vary in size a lot unfortunately --> |
| 110 <has_size value="50000" delta="10000" /> | 111 <has_size value="5000" delta="1000" /> |
| 111 </assert_contents> | 112 </assert_contents> |
| 112 </output> | 113 </output> |
| 113 </test> | 114 </test> |
| 114 <test> | 115 <test> |
| 115 <param name="gro_input" value="solv_ions.gro" /> | 116 <param name="gro_input" value="str_ions.gro" /> |
| 116 <param name="top_input" value="topol_solv.top" /> | 117 <param name="top_input" value="topol_solv.top" /> |
| 117 <param name="mdpfile" value="custom" /> | 118 <param name="mdpfile" value="custom" /> |
| 118 <param name="mdp_input" value="minim.mdp" /> | 119 <param name="mdp_input" value="minim.mdp" /> |
| 119 <output name="output1" ftype="gro" > | 120 <output name="output1" ftype="gro" > |
| 120 <assert_contents> | 121 <assert_contents> |
| 121 <has_size value="1726975" /> | 122 <has_size value="4281" /> |
| 122 </assert_contents> | 123 </assert_contents> |
| 123 </output> | 124 </output> |
| 124 <output name="output2" ftype="edr" > | 125 <output name="output2" ftype="edr" > |
| 125 <assert_contents> | 126 <assert_contents> |
| 126 <!-- this binary can vary in size a lot unfortunately --> | 127 <!-- this binary can vary in size a lot unfortunately --> |
| 127 <has_size value="50000" delta="10000" /> | 128 <has_size value="5000" delta="1000" /> |
| 128 </assert_contents> | 129 </assert_contents> |
| 129 </output> | 130 </output> |
| 130 </test> | 131 </test> |
| 131 | 132 |
| 132 </tests> | 133 </tests> |