Mercurial > repos > chemteam > gmx_sim
diff sim.xml @ 9:a97dcfc23b4b draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
| author | chemteam |
|---|---|
| date | Wed, 20 May 2020 13:00:42 -0400 |
| parents | 171ce1253b19 |
| children | f197e34c33a9 |
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--- a/sim.xml Fri May 08 07:41:18 2020 -0400 +++ b/sim.xml Wed May 20 13:00:42 2020 -0400 @@ -1,7 +1,8 @@ -<tool id="gmx_sim" name="GROMACS simulation" version="@VERSION@.1"> +<tool id="gmx_sim" name="GROMACS simulation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>for system equilibration or data collection</description> <macros> <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @@ -43,8 +44,16 @@ -o outp.tpr &>> verbose.txt && - gmx mdrun -nt "\${GALAXY_SLOTS:-4}" -deffnm outp &>> verbose.txt - + gmx mdrun + -nt "\${GALAXY_SLOTS:-4}" + ## GPU + #if "\${GROMACS_GPU:-0}" == 1: + -ntmpi 1 + -nb gpu + -pme gpu + #end if + -deffnm outp &>> verbose.txt + #if $outps.str == 'pdb' or $outps.str == 'both' && gmx editconf -f outp.gro -o outp.pdb &>> verbose.txt #end if @@ -259,7 +268,7 @@ <tests> <test expect_num_outputs="3"> - <param name="gro_input" value="npt.gro" /> + <param name="gro_input" value="str_ions.gro" /> <param name="top_input" value="topol_solv.top" /> <!-- <param name="cpt_bool" value="yes" /> --> <param name="cpt_in" value="npt.cpt" /> @@ -271,23 +280,27 @@ <param name="tpr_out" value="true"/> <param name="ensemble" value="npt" /> <!-- <param name="posres_bool" value="false" /> --> - <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> - <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> - <output name="output8" file="md_0_1.tpr" ftype="binary" compare="sim_size"/> - <!-- <output name="output1" ftype="gro"> + <output name="output1" ftype="gro"> <assert_contents> - <has_size value="2647999" /> + <has_size value="6537" /> + <has_n_lines n="97" /> + <has_line line="TEST in water" /> </assert_contents> </output> <output name="output3" ftype="trr"> <assert_contents> - <has_size value="10132584" /> + <has_size value="26136" /> </assert_contents> - </output> --> + </output> + <output name="output8" ftype="binary"> + <assert_contents> + <has_size value="44164" /> + </assert_contents> + </output> </test> <test expect_num_outputs="3"> - <param name="gro_input" value="npt.gro" /> + <param name="gro_input" value="str_ions.gro" /> <param name="top_input" value="topol_solv.top" /> <!-- <param name="cpt_bool" value="yes" /> --> <param name="cpt_in" value="npt.cpt" /> @@ -297,13 +310,30 @@ <expand macro="test_params"/> <param name="ensemble" value="npt" /> <!-- <param name="posres_bool" value="false" /> --> - <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> - <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> - <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> + <output name="output1" ftype="gro"> + <assert_contents> + <has_size value="6537" /> + <has_n_lines n="97" /> + <has_line line="TEST in water" /> + </assert_contents> + </output> + <output name="output2" ftype="pdb"> + <assert_contents> + <has_size value="7582" /> + <has_n_lines n="100" /> + <has_line line="TITLE TEST in water" /> + <has_line line="REMARK THIS IS A SIMULATION BOX" /> + </assert_contents> + </output> + <output name="output3" ftype="trr"> + <assert_contents> + <has_size value="26136" /> + </assert_contents> + </output> </test> <test expect_num_outputs="3"> - <param name="gro_input" value="npt.gro" /> + <param name="gro_input" value="str_ions.gro" /> <param name="top_input" value="topol_solv.top" /> <!-- <param name="cpt_bool" value="yes" /> --> <param name="cpt_in" value="npt.cpt" /> @@ -314,13 +344,30 @@ <expand macro="test_params"/> <param name="ensemble" value="npt" /> <!-- <param name="posres_bool" value="false" /> --> - <output name="output1" file="md_0_1.gro" ftype="gro" compare="sim_size"/> - <output name="output2" file="md_0_1.pdb" ftype="pdb" compare="sim_size"/> - <output name="output3" file="md_0_1.trr" ftype="trr" compare="sim_size"/> + <output name="output1" ftype="gro" compare="sim_size"> + <assert_contents> + <has_size value="6537" /> + <has_n_lines n="97" /> + <has_line line="TEST in water" /> + </assert_contents> + </output> + <output name="output2" ftype="pdb" compare="sim_size"> + <assert_contents> + <has_size value="7582" /> + <has_n_lines n="100" /> + <has_line line="TITLE TEST in water" /> + <has_line line="REMARK THIS IS A SIMULATION BOX" /> + </assert_contents> + </output> + <output name="output3" ftype="trr" compare="sim_size"> + <assert_contents> + <has_size value="26136" /> + </assert_contents> + </output> </test> <test expect_num_outputs="3"> - <param name="gro_input" value="em.gro" /> + <param name="gro_input" value="str_ions.gro" /> <param name="top_input" value="topol_solv.top" /> <!-- <param name="posres_bool" value="true" /> --> <param name="itp_in" value="posres.itp" /> @@ -332,9 +379,24 @@ <param name="ensemble" value="nvt" /> <expand macro="test_params"/> - <output name="output2" file="nvt.pdb" ftype="pdb" compare="sim_size"/> - <output name="output4" file="nvt.xtc" ftype="xtc" compare="sim_size"/> - <output name="output5" file="nvt.cpt" ftype="cpt" compare="sim_size"/> + <output name="output2" ftype="pdb"> + <assert_contents> + <has_size value="7582" /> + <has_n_lines n="100" /> + <has_line line="TITLE TEST in water" /> + <has_line line="REMARK THIS IS A SIMULATION BOX" /> + </assert_contents> + </output> + <output name="output4" ftype="xtc"> + <assert_contents> + <has_size value="4910" delta="20"/> + </assert_contents> + </output> + <output name="output5" ftype="cpt"> + <assert_contents> + <has_size value="3350" delta="20"/> + </assert_contents> + </output> </test> </tests>