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annotate trj.xml @ 1:e9cc595562b8 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"
author chemteam
date Thu, 13 Feb 2020 03:51:40 -0500
parents bb0053c4e4f2
children 9363254ef848
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bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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1 <tool id="gmx_trj" name="Modify/convert GROMACS trajectories" version="@VERSION@">
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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2 <description>using trjconv and trjcat</description>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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3 <macros>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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4 <import>macros.xml</import>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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5 </macros>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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7 <expand macro="requirements" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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8
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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9 <command detect_errors="exit_code"><![CDATA[
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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11 #if $trj.trj_op == 'trjcat':
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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12 mkdir trajs &&
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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13 #for $value, $file in enumerate($trj_input):
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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14 ln -s '$file' trajs/traj_${value}.${file.ext} &&
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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15 #end for
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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16
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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17 gmx trjcat
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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18 -f trajs/traj* ## here we assume that they all have the same ext, probably reasonable
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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19 $trj.cat
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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20 -e '$time.e'
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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21
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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22 #elif $trj.trj_op == 'trjconv':
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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23 ln -s '$ndx_input' ./index.ndx &&
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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24 ln -s '$str_input' ./str.${str_input.ext} &&
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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25 ln -s '$trj_input' ./traj.${trj_input.ext} &&
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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26 #if $trj.center:
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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27 echo '$trj.index_center $trj.index_output' | gmx trjconv
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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28 #else
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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29 echo '$trj.index_output' | gmx trjconv
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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30 #end if
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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31 -f ./traj.${trj_input.ext}
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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32 -s ./str.${str_input.ext}
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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33 -n ./index.ndx
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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34 $trj.center
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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35 -pbc $trj.pbc
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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36 -ur $trj.ur
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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37 -boxcenter $trj.boxcenter
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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38 #if $time.e != -1:
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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39 -e '$time.e'
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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40 #end if
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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41
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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42 #end if
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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43
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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44 -b '$time.b'
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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45 -dt '$time.dt'
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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46 -o ./output.${output_format} &&
1
e9cc595562b8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"
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47 &>> verbose.txt &&
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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48 mv ./output.${output_format} '$output'
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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49
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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50 ]]></command>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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51
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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52 <inputs>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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53 <conditional name="trj">
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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54 <param name="trj_op" type="select" label="Modify a trajectory or concatenate multiple trajectories?">
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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55 <option value="trjconv">Modify (trjconv)</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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56 <option value="trjcat">Concatenate (trjcat)</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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57 </param>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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58 <when value="trjconv">
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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59 <param name="trj_input" type="data" format='xtc,trr' label="Input trajectory" help="In XTC or TRR format."/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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60 <param name="str_input" type="data" format='pdb,gro,tpr' label="Input structure" help="In PDB, GRO or TPR format."/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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61 <param name="ndx_input" type="data" format='ndx' label="Index (NDX) file" help="In NDX format."/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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62 <param name="index_output" type="text" label="Index of group to save in the output" help="Index of group to save in the output - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).">
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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63 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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64 </param>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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65 <param name="center" type="boolean" label="Center system in box" truevalue="-center" falsevalue=""/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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66 <param name="index_center" type="text" label="Index of group for centering" optional="true" help="Index of group for centering - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0). Leave blank if centering is not required.">
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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67 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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68 </param>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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69 <param name="pbc" type="select" label="PBC treatment" >
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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70 <option value="none">none</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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71 <option value="mol">mol</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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72 <option value="res">res</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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73 <option value="atom">atom</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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74 <option value="nojump">nojump</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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75 <option value="cluster">cluster</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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76 <option value="whole">whole</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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77 </param>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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78 <param name="ur" type="select" label="Unit cell representation" >
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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79 <option value="rect">rect</option>
1
e9cc595562b8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"
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80 <option value="tric">tric</option>
e9cc595562b8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"
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81 <option value="compact">compact</option>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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82 </param>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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83 <param name="boxcenter" type="select" label="Center for PBC and centering treatment" >
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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84 <option value="rect">rect</option>
1
e9cc595562b8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"
chemteam
parents: 0
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85 <option value="tric" selected="true">tric</option>
e9cc595562b8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"
chemteam
parents: 0
diff changeset
86 <option value="zero">zero</option>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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87 </param>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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88 </when>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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89 <when value="trjcat">
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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90 <param name="trj_input" type="data" format='xtc,trr' label="Input trajectories" help="In XTC or TRR format, but please do not mix the two. Please note this tool does not currently take order into account when concatenating." multiple="true"/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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91 <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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92 </when>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
parents:
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93 </conditional>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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94 <param name="output_format" type="select" label="Output format" >
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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95 <option value="xtc">XTC</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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96 <option value="trr">TRR</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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97 <option value="pdb">PDB</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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98 <option value="gro">GRO</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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99 </param>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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100 <section title="Time" name='time' expanded="true">
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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101 <param name="b" type="integer" label="Start time" help="Time (ps) of first frame to read from trajectory" value="0" min="0"/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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102 <param name="e" type="integer" label="End time" help="Time (ps) of last frame to read from trajectory" value="-1" min="-1"/> <!-- stupidly this has different default values for trjconv and trjcat -->
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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103 <param name="dt" type="integer" label="Write frames at this time interval (ps)" help="Only write frame when t is exactly divisible by this value. Leave as 0 to record all frames." value="0" min="0"/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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104 </section>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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105 <expand macro="log" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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106 </inputs>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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107 <outputs>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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108 <data name="output" format="xtc">
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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109 <change_format>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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110 <when input="output_format" value="trr" format="trr"/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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111 <when input="output_format" value="xtc" format="xtc"/>
1
e9cc595562b8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"
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112 <when input="output_format" value="gro" format="gro"/>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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113 <when input="output_format" value="pdb" format="pdb"/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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114 </change_format>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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115 </data>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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116 </outputs>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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117 <tests>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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118 <test>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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119 <!-- gmx trjcat -f npt.xtc nvt.xtc -cat -o test.xtc -->
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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120 <param name="trj_op" value="trjcat" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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121 <param name="trj_input" value="npt.xtc,nvt.xtc" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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122 <param name="b" value="0" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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123 <param name="e" value="-1" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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124 <param name="dt" value="0" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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125 <param name="cat" value="true" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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126 <output name="output" file="trjcat.xtc" ftype="xtc"/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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127 </test>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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128 <test>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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129 <!-- echo '1 1' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -o npt_c.xtc -->
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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130 <param name="trj_op" value="trjconv" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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131 <param name="trj_input" value="npt.xtc" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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132 <param name="str_input" value="npt.tpr" ftype="tpr"/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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133 <param name="ndx_input" value="index.ndx" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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134 <param name="b" value="0" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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135 <param name="e" value="-1" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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diff changeset
136 <param name="dt" value="0" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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137 <param name="index_output" value="1" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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138 <param name="index_center" value="1" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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139 <param name="center" value="true" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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140 <param name="pbc" value="mol" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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141 <param name="ur" value="compact" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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142 <param name="ur" value="tric" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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143 <output name="output" file="trjconv.xtc" ftype="xtc"/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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144 </test>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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145 </tests>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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146 <help><![CDATA[
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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147
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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148 .. class:: infomark
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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149
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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150 **What it does**
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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151
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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152 This tool allows manipulation of GROMACS trajectories, drawing on the trjcat and trjconv commands.
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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153
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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154 _____
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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155
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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156
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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diff changeset
157 .. class:: infomark
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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158
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
chemteam
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159 **Input**
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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160
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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161 - One or more trajectory file (XTC or TRR)
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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162 - Structure file (optional)
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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163 - Various options can be set
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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164
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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165 _____
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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166
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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167
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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168 .. class:: infomark
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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169
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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170 **Output**
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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171
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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172 - GROMACS trajectory or structure file (XTC, TRR, PDB, GRO)
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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173
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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174
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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175 ]]></help>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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176 <expand macro="citations" />
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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177 </tool>