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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
author agpetit
date Thu, 21 Jul 2022 14:46:22 +0000
parents ae4b0af8efd3
children
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ae4b0af8efd3 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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1 <tool id="gmx_check" name="GROMACS check" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="@PROFILE@">
2
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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2 <description>to provide information about GROMACS input files</description>
0
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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3 <macros>
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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4 <token name="@GALAXY_VERSION@">0</token>
1
ae4b0af8efd3 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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5 <token name="@PROFILE@">21.05</token>
0
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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6 <import>macros.xml</import>
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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7 </macros>
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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8 <expand macro="requirements" />
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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9 <command detect_errors="exit_code"><![CDATA[
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8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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10 #if $input_file.calculate_select == "info_traj":
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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11 ln -s '$input_file.traj_file' './traj.$input_file.traj_file.ext';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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12 gmx check
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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13 -f './traj.$input_file.traj_file.ext'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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14 &> '$out_info_traj';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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15 #elif $input_file.calculate_select == "compare_traj":
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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16 ln -s '$input_file.traj_file' './traj1.$input_file.traj_file.ext';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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17 ln -s '$input_file.traj_file2' './traj2.$input_file.traj_file2.ext';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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18 gmx check
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19 -f './traj1.$input_file.traj_file.ext'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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20 -f2 './traj2.$input_file.traj_file2.ext'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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21 $input_file.rmsd
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22 -tol '$input_file.rel_tol'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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23 -abstol '$input_file.abs_tol'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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24 &> '$out_compare_traj';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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25 #elif $input_file.calculate_select == "info_struc":
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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26 ln -s '$input_file.struc_file' './struc.$input_file.struc_file.ext';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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27 gmx check
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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28 -c './struc.$input_file.struc_file.ext'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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29 -vdwfac '$input_file.vdwfac'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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30 -bonlo '$input_file.bonlo'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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31 -bonhi '$input_file.bonhi'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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32 &> '$out_info_struc';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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33 #elif $input_file.calculate_select == "info_ener":
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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34 ln -s '$input_file.ener_file' './ener.$input_file.ener_file.ext' ;
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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35 gmx check
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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36 -e './ener.$input_file.ener_file.ext'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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37 &> '$out_info_ener';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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38 #elif $input_file.calculate_select == "info_ind":
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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39 ln -s '$input_file.ind_file' './index.$input_file.ind_file.ext';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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40 gmx check
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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41 -n './index.$input_file.ind_file.ext'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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42 &> '$out_info_ind';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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43 #elif $input_file.calculate_select == "compare_ener":
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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44 ln -s '$input_file.ener_file' './ener1.$input_file.ener_file.ext';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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45 ln -s '$input_file.ener_file2' './ener2.$input_file.ener_file2.ext';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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46 gmx check
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47 -e './ener1.$input_file.ener_file.ext'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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48 -e2 './ener2.$input_file.ener_file2.ext'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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49 -tol '$input_file.rel_tol'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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50 -abstol '$input_file.abs_tol'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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51 -lastener '$input_file.lastener'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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52 &> '$out_compare_ener';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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53 #else:
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54 ln -s '$input_file.top_file' './top1.$input_file.top_file.ext';
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55 ln -s '$input_file.top_file2' './top2.$input_file.top_file2.ext';
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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56 gmx check
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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57 -s1 './top1.$input_file.top_file.ext'
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58 -s2 './top2.$input_file.top_file2.ext'
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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59 -abstol '$input_file.abs_tol'
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60 &> '$out_compare_topol';
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61 #end if
0
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62 ]]></command>
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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63 <inputs>
2
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64 <conditional name="input_file">
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65 <param name="calculate_select" type="select" label="Select the type of information you want to obtain">
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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66 <option value="info_traj">Information about a trajectory</option>
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67 <option value="compare_traj">Compare two trajectories</option>
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68 <option value="info_struc">Information about the system structure</option>
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69 <option value="info_ener">Information about the system energy</option>
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70 <option value="info_ind">Information about the system index</option>
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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71 <option value="compare_top">Compare two topologies</option>
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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72 <option value="compare_ener">Compare two energy files</option>
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73 </param>
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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74 <when value="info_traj">
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75 <param name="traj_file" type="data" format="xtc, trr, cpt, gro, pdb" label="Trajectory file" help="Enter the trajectory file. Accepted formats: xtc, trr, cpt, gro, pdb."/>
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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76 </when>
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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77 <when value="compare_traj">
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78 <param name="traj_file" type="data" format="xtc, trr, cpt, gro, pdb" label="Trajectory file 1" help="Enter the first trajectory file. Accepted formats: xtc, trr, cpt, gro, pdb."/>
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79 <param name="traj_file2" type="data" format="xtc, trr, cpt, gro, pdb" label="Trajectory file 2" help="Enter the second trajectory file. Accepted formats: xtc, trr, cpt, gro, pdb."/>
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80 <param name="rmsd" type="boolean" truevalue="-rmsd" falsevalue="" label="Do you want to display the RMSD?"/>
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81 <param name="rel_tol" type="float" max="1.0" value="0.001" label="Enter relative tolerance" help="Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)."/>
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82 <param name="abs_tol" type="float" max="1.0" value="0.001" optional="True" label="Enter absolute tolerance" help="Absolute tolerance, useful when sums are close to zero."/>
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83 </when>
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84 <when value="info_struc">
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85 <param name="struc_file" type="data" format="tpr, gro, pdb, brk, ent" label="Structure file" help="Enter the structure file. Accepted formats: tpr, gro, pdb, brk, ent.">
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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86 <validator type="expression" message="Wrong file format">value.extension != 'edr' and value.extension != 'xtc'</validator>
0
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87 </param>
2
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88 <param name="vdwfac" type="float" max="1.0" min="0" value="0.8" label="Enter the fraction of sum of VdW radii sum"/>
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89 <param name="bonlo" type="float" max="1.0" min="0" value="0.4" label="Enter the minimal fraction of sum of van der Waals radii for bonded atoms"/>
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90 <param name="bonhi" type="float" max="1.0" min="0" value="0.7" label="Enter the maximal fraction of sum of van der Waals radii for bonded atoms"/>
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91 </when>
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92 <when value="info_ener">
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93 <param name="ener_file" type="data" format="edr" label="Energy file" help="Enter the energy file. Accepted format: edr."/>
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94 </when>
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95 <when value="info_ind">
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96 <param name="ind_file" type="data" format="ndx" label="Index file" help="Enter the index file. Accepted format: ndx."/>
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97 </when>
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98 <when value="compare_top">
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99 <param name="top_file" type="data" format="tpr" label="Topology file 1" help="Enter the first topology file. Accepted format: tpr.">
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100 <validator type="expression" message="Wrong file format">value.extension == 'tpr'</validator>
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101 </param>
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102 <param name="top_file2" type="data" format="tpr" label="Topology file 2" help="Enter the second topology file. Accepted format: tpr.">
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103 <validator type="expression" message="Wrong file format">value.extension == 'tpr'</validator>
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104 </param>
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105 <param name="abs_tol" type="float" max="1.0" value="0.001" label="Enter absolute tolerance" help="Absolute tolerance, useful when sums are close to zero."/>
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106 </when>
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107 <when value="compare_ener">
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108 <param name="ener_file" type="data" format="edr" label="Energy file 1" help="Enter the first energy file. Accepted format: edr."/>
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109 <param name="ener_file2" type="data" format="edr" label="Energy file 2" help="Enter the second energy file. Accepted format: edr."/>
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110 <param name="rel_tol" type="float" max="1.0" value="0.001" label="Enter relative tolerance" help="Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)."/>
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111 <param name="abs_tol" type="float" max="1.0" value="0.001" optional="True" label="Enter absolute tolerance" help="Absolute tolerance, useful when sums are close to zero."/>
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112 <param name="lastener" type="text" value="all" label="Enter the last energy term to compare" help="Last energy term to compare. It makes sense to go up until the Pressure."/>
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113 </when>
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114 </conditional>
0
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115 </inputs>
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116 <outputs>
2
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117 <data name="out_info_traj" format="txt" from_work_dir="*.txt" label="${tool.name} : information on trajectory on ${on_string}">
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118 <filter>input_file["calculate_select"] == "info_traj"</filter>
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119 </data>
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120 <data name="out_compare_traj" format="txt" from_work_dir="*.txt" label="${tool.name} : compare trajectories on ${on_string}">
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121 <filter>input_file["calculate_select"] == "compare_traj"</filter>
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122 </data>
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123 <data name="out_info_struc" format="txt" from_work_dir="*.txt" label="${tool.name} : information on structure on ${on_string}">
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124 <filter>input_file["calculate_select"] == "info_struc"</filter>
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125 </data>
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126 <data name="out_info_ener" format="txt" from_work_dir="*.txt" label="${tool.name} : information on energy on ${on_string}">
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127 <filter>input_file["calculate_select"] == "info_ener"</filter>
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128 </data>
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129 <data name="out_info_ind" format="txt" from_work_dir="*.txt" label="${tool.name} : information on index file on ${on_string}">
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130 <filter>input_file["calculate_select"] == "info_ind"</filter>
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131 </data>
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132 <data name="out_compare_ener" format="txt" from_work_dir="*.txt" label="${tool.name} : compare energy files on ${on_string}">
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133 <filter>input_file["calculate_select"] == "compare_ener"</filter>
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134 </data>
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135 <data name="out_compare_topol" format="txt" from_work_dir="*.txt" label="${tool.name} : compare topology files on ${on_string}">
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136 <filter>input_file["calculate_select"] == "compare_top"</filter>
0
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137 </data>
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138 </outputs>
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139 <tests>
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140 <test>
2
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141 <conditional name="input_file">
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142 <param name="calculate_select" value="info_traj"/>
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143 <param name="traj_file" value="nvt.xtc" ftype="xtc"/>
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144 </conditional>
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145 <output name="out_info_traj" file="check_info_traj.txt" ftype="txt" lines_diff="8"/>
0
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146 </test>
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147 <test>
2
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148 <conditional name="input_file">
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149 <param name="calculate_select" value="compare_traj"/>
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150 <param name="traj_file" value="nvt.xtc" ftype="xtc"/>
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151 <param name="traj_file2" value="npt.xtc" ftype="xtc"/>
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152 <param name="rmsd" value="True"/>
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153 <param name="rel_tol" value="0.1"/>
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154 <param name="abs_tol" value="0.1"/>
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155 </conditional>
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156 <output name="out_compare_traj" file="check_compare_traj.txt" ftype="txt" lines_diff="8"/>
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157 </test>
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158 <test>
2
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159 <conditional name="input_file">
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160 <param name="calculate_select" value="info_struc"/>
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161 <param name="struc_file" value="minim.gro" ftype="gro"/>
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162 <param name="vdwfac" value="0.8"/>
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163 <param name="bonlo" value="0.4"/>
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164 <param name="bonhi" value="0.7"/>
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165 </conditional>
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166 <output name="out_info_struc" file="check_info_structure.txt" ftype="txt" lines_diff="10"/>
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167 </test>
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168 <test>
2
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169 <conditional name="input_file">
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170 <param name="calculate_select" value="info_ener"/>
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171 <param name="ener_file" value="minim.edr" ftype="edr"/>
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172 </conditional>
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173 <output name="out_info_ener" file="check_info_energy.txt" ftype="txt" lines_diff="8"/>
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174 </test>
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175 <test>
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176 <conditional name="input_file">
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177 <param name="calculate_select" value="info_ind"/>
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178 <param name="ind_file" value="index.ndx" ftype="ndx"/>
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179 </conditional>
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180 <output name="out_info_ind" file="check_info_index.txt" ftype="txt" lines_diff="8"/>
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181 </test>
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182 <test>
2
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183 <conditional name="input_file">
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184 <param name="calculate_select" value="compare_top"/>
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185 <param name="top_file" value="npt.tpr" ftype="tpr"/>
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186 <param name="top_file2" value="npt2.tpr" ftype="tpr"/>
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187 <param name="abs_tol" value="0.1"/>
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188 </conditional>
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189 <output name="out_compare_topol" file="check_compare_topology.txt" ftype="txt" lines_diff="8"/>
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190 </test>
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191 <test>
2
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192 <conditional name="input_file">
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193 <param name="calculate_select" value="compare_ener"/>
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194 <param name="ener_file" value="minim.edr" ftype="edr"/>
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195 <param name="ener_file2" value="outp.edr" ftype="edr"/>
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196 <param name="rel_tol" value="0.1"/>
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197 <param name="abs_tol" value="0.1"/>
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198 <param name="lastener" value="Pressure"/>
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199 </conditional>
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200 <output name="out_compare_ener" file="check_compare_energy.txt" ftype="txt" lines_diff="8"/>
0
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201 </test>
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202 </tests>
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203 <help><![CDATA[
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204
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205 .. class:: infomark
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206
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207 **What it does**
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208
2
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209 This tool reads a trajectory (trr or xtc), an energy file (edr) or an index file (ndx) and prints out useful information about them.
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210
2
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211 Selecting 'information about the structure of a system' checks for the presence of coordinates, velocities and the box in the file, close contacts (smaller than van der Waals radii and not bound, i.e. not between minimal fraction of sum of van der Waals radii and maximal fraction of sum of van der Waals radii, all relative to the sum of the two van der Waals radii) and atoms outside the box (these can occur often and are not a problem). If velocities are present, an estimated temperature will be calculated from them.
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212
2
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213 If an index file is given, its contents will be summarized.
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214
2
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215 The program can compare two runtime input files (tpr) when both topology file 1 and topology file 2 are provided. When comparing run input files this way, the default relative tolerance is reduced to 0.000001 and the absolute tolerance set to zero to find any differences not due to minor compiler optimization differences, although you can of course still set any other tolerances through the options. Similarly a pair of trajectory files can be compared (using compare two trajectories), or a pair of energy files (using compare two energy files).
0
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216
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217 _____
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218
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219 .. class:: infomark
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220
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221 **Inputs**
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222
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223 **Information about a trajectory**
2
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224 - Trajectory file : trajectory file in xtc, trr, cpt, gro or pdb format.
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225
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226 **Compare two trajectories**
2
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227 - Trajectory file 1 : trajectory file in xtc, trr, cpt, gro or pdb format.
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228 - Trajectory file 2 : trajectory file in xtc, trr, cpt, gro or pdb format.
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229 - Do you want to display the RMSD? : print RMSD for x, v and f.
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230 - Enter relative tolerance : relative tolerance for comparing real values.
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231 - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero.
0
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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232
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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233 **Information about the structure of a system**
2
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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234 - Structure file : structure file in tpr, gro, pdb, brk or ent format.
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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235 - Enter the fraction of sum of VdW radii : fraction of sum of VdW radii used as warning cutoff.
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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236 - Enter the minimal fraction of sum of van der Waals radii for bonded atoms : minimal fraction of sum of van der Waals radii for bonded atoms.
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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237 - Enter the maximal fraction of sum of van der Waals radii for bonded atoms : maximal fraction of sum of van der Waals radii for bonded atoms.
0
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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238
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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239 **Information about the energy of a system**
2
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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240 - Energy file : energy file in edr format.
0
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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241
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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242 **Information about the index of a system**
2
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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243 - Index file : index file in ndx format.
0
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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244
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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245 **Compare two topologies**
2
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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246 - Topology file 1 : topology file in tpr format.
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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247 - Topology file 2 : topology file in tpr format.
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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248 - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero.
0
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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249
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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250 **Compare two energy files**
2
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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251 - Energy file 1 : energy file in edr format.
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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252 - Energy file 2 : energy file in edr format.
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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253 - Enter relative tolerance : relative tolerance for comparing real values.
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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254 - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero.
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
agpetit
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255 - Enter the last energy term to compare : last energy term to compare (if not given all are tested). It makes sense to go up until the pressure.
0
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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256
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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257 _____
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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258
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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259 .. class:: infomark
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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260
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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261 **Output**
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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262
2
8ee4590690e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 11dcfa0a6d5fbff9bc654a8a1ad14d79dbd22fdb"
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263 - list with one or more text files. This file contains either information about the trajectory, the structure, the index or the energy, or a comparison between two trajectories, two topologies or two energy files.
0
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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264
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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265 ]]></help>
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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266 <citations>
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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267 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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268 </citations>
abafe01a9fc2 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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269 </tool>