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comparison minim.xml @ 12:8ed0f32c77f1 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 16:50:24 +0000
parents 5de8b11fe8df
children
comparison
equal deleted inserted replaced
11:5de8b11fe8df 12:8ed0f32c77f1
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>