annotate check.xml @ 0:26467f738ed4 draft

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
author chemteam
date Tue, 12 Jul 2022 12:48:09 +0000
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26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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1 <tool id="gmx_check" name="GROMACS check" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="@PROFILE@">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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2 <description>to provide information about GROMACS input files</description>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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3 <macros>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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4 <token name="@GALAXY_VERSION@">0</token>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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5 <token name="@PROFILE@">21.05</token>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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6 <import>macros.xml</import>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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7 </macros>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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8 <expand macro="requirements" />
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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9 <command detect_errors="exit_code"><![CDATA[
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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10 #if $input_file.calculate_select == "info_traj":
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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11 ln -s '$input_file.traj_file' './traj.$input_file.traj_file.ext' &&
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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12 gmx check
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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13 -f './traj.$input_file.traj_file.ext'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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14 &> '$out_info_traj'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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15 #elif $input_file.calculate_select == "compare_traj":
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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16 ln -s '$input_file.traj_file' './traj1.$input_file.traj_file.ext' &&
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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17 ln -s '$input_file.traj_file2' './traj2.$input_file.traj_file2.ext' &&
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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18 gmx check
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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19 -f './traj1.$input_file.traj_file.ext'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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20 -f2 './traj2.$input_file.traj_file2.ext'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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21 $input_file.rmsd
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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22 -tol '$input_file.rel_tol'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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23 -abstol '$input_file.abs_tol'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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24 &> '$out_compare_traj'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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25 #elif $input_file.calculate_select == "info_struc":
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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26 ln -s '$input_file.struc_file' './struc.$input_file.struc_file.ext' &&
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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27 gmx check
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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28 -c './struc.$input_file.struc_file.ext'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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29 -vdwfac '$input_file.vdwfac'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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30 -bonlo '$input_file.bonlo'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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31 -bonhi '$input_file.bonhi'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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32 &> '$out_info_struc'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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33 #elif $input_file.calculate_select == "info_ener":
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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34 ln -s '$input_file.ener_file' './ener.$input_file.ener_file.ext' &&
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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35 gmx check
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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36 -e './ener.$input_file.ener_file.ext'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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37 &> '$out_info_ener'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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38 #elif $input_file.calculate_select == "info_ind":
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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39 ln -s '$input_file.ind_file' './index.$input_file.ind_file.ext' &&
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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40 gmx check
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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41 -n './index.$input_file.ind_file.ext'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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42 &> '$out_info_ind'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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43 #elif $input_file.calculate_select == "compare_ener":
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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44 ln -s '$input_file.ener_file' './ener1.$input_file.ener_file.ext' &&
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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45 ln -s '$input_file.ener_file2' './ener2.$input_file.ener_file2.ext' &&
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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46 gmx check
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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47 -e './ener1.$input_file.ener_file.ext'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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48 -e2 './ener2.$input_file.ener_file2.ext'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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49 -tol '$input_file.rel_tol'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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50 -abstol '$input_file.abs_tol'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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51 -lastener '$input_file.lastener'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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52 &> '$out_compare_ener'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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53 #else:
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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54 ln -s '$input_file.top_file' './top1.$input_file.top_file.ext' &&
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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55 ln -s '$input_file.top_file2' './top2.$input_file.top_file2.ext'&&
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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56 gmx check
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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57 -s1 './top1.$input_file.top_file.ext'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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58 -s2 './top2.$input_file.top_file2.ext'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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59 -abstol '$input_file.abs_tol'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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60 &> '$out_compare_topol'
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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61 #end if
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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62 ]]></command>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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63 <inputs>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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64 <conditional name="input_file">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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65 <param name="calculate_select" type="select" label="Select the type of information you want to obtain">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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66 <option value="info_traj">Information about a trajectory</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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67 <option value="compare_traj">Compare two trajectories</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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68 <option value="info_struc">Information about the system structure</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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69 <option value="info_ener">Information about the system energy</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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70 <option value="info_ind">Information about the system index</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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71 <option value="compare_top">Compare two topologies</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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72 <option value="compare_ener">Compare two energy files</option>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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73 </param>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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74 <when value="info_traj">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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76 </when>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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77 <when value="compare_traj">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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80 <param name="rmsd" type="boolean" truevalue="-rmsd" falsevalue="" label="Do you want to display the RMSD?"/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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|)."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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83 </when>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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84 <when value="info_struc">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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.">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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diff changeset
86 <validator type="expression" message="Wrong file format">value.extension != 'edr' and value.extension != 'xtc'</validator>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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87 </param>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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88 <param name="vdwfac" type="float" max="1.0" value="0.8" label="Enter the fraction of sum of VdW radii sum"/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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89 <param name="bonlo" type="float" max="1.0" value="0.4" label="Enter the minimal fraction of sum of van der Waals radii for bonded atoms"/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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90 <param name="bonhi" type="float" max="1.0" value="0.7" label="Enter the maximal fraction of sum of van der Waals radii for bonded atoms"/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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91 </when>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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92 <when value="info_ener">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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93 <param name="ener_file" type="data" format="edr" label="Energy file" help="Enter the energy file. Accepted format: edr."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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94 </when>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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95 <when value="info_ind">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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96 <param name="ind_file" type="data" format="ndx" label="Index file" help="Enter the index file. Accepted format: ndx."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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97 </when>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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98 <when value="compare_top">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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.">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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100 <validator type="expression" message="Wrong file format">value.extension == 'tpr'</validator>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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101 </param>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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.">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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103 <validator type="expression" message="Wrong file format">value.extension == 'tpr'</validator>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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104 </param>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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106 </when>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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|)."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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."/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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113 </when>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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114 </conditional>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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115 </inputs>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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116 <outputs>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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117 <data name="out_info_traj" format="txt" from_work_dir="*.txt" label="${tool.name} : information on trajectory on ${on_string}">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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118 <filter>input_file["calculate_select"] == "info_traj"</filter>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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119 </data>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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120 <data name="out_compare_traj" format="txt" from_work_dir="*.txt" label="${tool.name} : compare trajectories on ${on_string}">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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121 <filter>input_file["calculate_select"] == "compare_traj"</filter>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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122 </data>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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123 <data name="out_info_struc" format="txt" from_work_dir="*.txt" label="${tool.name} : information on structure on ${on_string}">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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124 <filter>input_file["calculate_select"] == "info_struc"</filter>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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125 </data>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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126 <data name="out_info_ener" format="txt" from_work_dir="*.txt" label="${tool.name} : information on energy on ${on_string}">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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127 <filter>input_file["calculate_select"] == "info_ener"</filter>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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128 </data>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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129 <data name="out_info_ind" format="txt" from_work_dir="*.txt" label="${tool.name} : information on index file on ${on_string}">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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130 <filter>input_file["calculate_select"] == "info_ind"</filter>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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131 </data>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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132 <data name="out_compare_ener" format="txt" from_work_dir="*.txt" label="${tool.name} : compare energy files on ${on_string}">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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133 <filter>input_file["calculate_select"] == "compare_ener"</filter>
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134 </data>
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135 <data name="out_compare_topol" format="txt" from_work_dir="*.txt" label="${tool.name} : compare topology files on ${on_string}">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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136 <filter>input_file["calculate_select"] == "compare_top"</filter>
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137 </data>
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138 </outputs>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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139 <tests>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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140 <test>
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141 <conditional name="input_file">
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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"/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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"/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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146 </test>
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147 <test>
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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"/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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152 <param name="rmsd" value="True"/>
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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>
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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>
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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>
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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>
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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"/>
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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
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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
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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
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213 If an index file is given, its contents will be summarized.
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214
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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).
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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**
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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**
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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.
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232
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233 **Information about the structure of a system**
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234 - Structure file : structure file in tpr, gro, pdb, brk or ent format.
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235 - Enter the fraction of sum of VdW radii : fraction of sum of VdW radii used as warning cutoff.
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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.
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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.
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238
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239 **Information about the energy of a system**
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240 - Energy file : energy file in edr format.
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241
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242 **Information about the index of a system**
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243 - Index file : index file in ndx format.
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244
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245 **Compare two topologies**
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246 - Topology file 1 : topology file in tpr format.
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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247 - Topology file 2 : topology file in tpr format.
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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248 - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero.
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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249
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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250 **Compare two energy files**
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251 - Energy file 1 : energy file in edr format.
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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252 - Energy file 2 : energy file in edr format.
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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253 - Enter relative tolerance : relative tolerance for comparing real values.
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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254 - Enter absolute tolerance : absolute tolerance, useful when sums are close to zero.
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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.
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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256
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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257 _____
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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258
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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259 .. class:: infomark
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260
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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261 **Output**
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262
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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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.
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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264
26467f738ed4 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 8660ff51cd1a65b04f862562957592fe152fc81d
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265 ]]></help>
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266 <citations>
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267 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
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268 </citations>
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269 </tool>