Mercurial > repos > chemteam > gmx_trj

annotate trj.xml @ 16:32052c6c3310 draft default tip

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
author chemteam
date Mon, 24 Oct 2022 22:36:40 +0000
parents 72459c3ea5f6
children
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rev   line source
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32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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1 <tool id="gmx_trj" name="Modify/convert and concatate GROMACS trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="21.09">
0
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>
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32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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5 <token name="@GALAXY_VERSION@">2</token>
5
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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6 <xml name="fit_when" token_option="none">
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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7 <when value="@OPTION@">
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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8 <param name="index_fit" type="text" label="Index of group to use for fitting" help="Index of group to use for fitting - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).">
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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9 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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10 </param>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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11 </when>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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12 </xml>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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13 </macros>
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32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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14 <expand macro="requirements"/>
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bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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15 <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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16 #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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17 mkdir trajs &&
16
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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18 #set $file_count = 0 ## sets 1st input to 0
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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19 #set $file_list = []
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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20 #for $file_count, $file in enumerate($trj_input): ## enumerates each input file, starting from 0
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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21 #set $filename = "trajs/traj_%i.%s" % ($file_count, $file.ext)
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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22 #silent $file_list.append($filename)
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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23 ln -s '$file' '$filename' &&
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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24 #end for
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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25
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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26 ## runs inputs from a repeat block. By choosing each input, this allows the user to select individual input files at a time, as well as ensure the proper order.
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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27 #for $traj_repeat in $trj.inputtrajs:
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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28 #for $file in $traj_repeat.trj_input:
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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29 #set $file_count = $file_count + 1 ## inputs from this repeat block will be numbered at + 1 ahead of inputs from first multiple select above
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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30 #set $filename = "trajs/traj_%i.%s" % ($file_count, $file.ext)
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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31 #silent $file_list.append($filename)
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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32 ln -s '$file' '$filename' &&
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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33 #end for
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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34 #end for
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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35
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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36 gmx trjcat
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32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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37 -f
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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38 #for $filename in $file_list:
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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39 '$filename'
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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40 #end for
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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41 $trj.cat
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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42 -e '$time.e'
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 #elif $trj.trj_op == 'trjconv':
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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45 ln -s '$ndx_input' ./index.ndx &&
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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46 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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47 ln -s '$trj_input' ./traj.${trj_input.ext} &&
5
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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48
14
72459c3ea5f6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 033779f5ae0fa964ccad44104027d1d715b8e907"
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49 echo ## optionally pipe in the following
72459c3ea5f6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 033779f5ae0fa964ccad44104027d1d715b8e907"
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50 #if $trj.fit.fit != 'none':
72459c3ea5f6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 033779f5ae0fa964ccad44104027d1d715b8e907"
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51 '$trj.fit.index_fit'
72459c3ea5f6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 033779f5ae0fa964ccad44104027d1d715b8e907"
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52 #end if
72459c3ea5f6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 033779f5ae0fa964ccad44104027d1d715b8e907"
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53 #if $trj.pbc.pbc == 'cluster':
72459c3ea5f6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 033779f5ae0fa964ccad44104027d1d715b8e907"
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54 '$trj.pbc.index_cluster'
72459c3ea5f6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 033779f5ae0fa964ccad44104027d1d715b8e907"
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55 #end if
72459c3ea5f6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 033779f5ae0fa964ccad44104027d1d715b8e907"
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56 '$trj.index_center' '$trj.index_output' | gmx trjconv
5
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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57 -f ./traj.${trj_input.ext}
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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58 -s ./str.${str_input.ext}
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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59 #if $ndx_input:
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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60 -n ./index.ndx
5
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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61 #end if
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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62 #if $trj.index_center:
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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63 -center
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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64 #end if
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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65 #if $trj.sep:
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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66 -sep
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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67 -nzero 9 ## hopefully the traj has < 1 bn frames, or collection order will be wrong
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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68 #end if
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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69 -pbc $trj.pbc.pbc
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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70 -ur $trj.ur
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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71 -boxcenter $trj.boxcenter
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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72 -fit $trj.fit.fit
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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73 #if $time.e != -1:
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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74 -e '$time.e'
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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75 #end if
16
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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76 #if $trj.skip:
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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77 -skip $trj.skip
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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78 #end if
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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79 #end if
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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80
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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81 -b '$time.b'
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82 -dt '$time.dt'
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83 -o ./output.${output_format}
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84 >> verbose.txt 2>&1
5
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85 #if not $trj.sep:
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86 &&
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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87 mv ./output.${output_format} '$output'
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88 #end if
0
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89 ]]></command>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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90 <inputs>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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91 <conditional name="trj">
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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92 <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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93 <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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94 <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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95 </param>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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96 <when value="trjconv">
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97 <param name="trj_input" type="data" format="xtc,trr,pdb,gro" label="Input trajectory" help="In XTC or TRR format; structure files with PDB or GRO format can also be used."/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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98 <param name="str_input" type="data" format="pdb,gro,tpr" label="Input structure" help="In PDB, GRO or TPR format."/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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99 <param name="ndx_input" type="data" format="ndx" label="Index (NDX) file" optional="true" help="In NDX format. Optional."/>
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100 <param name="index_output" value="0" 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).">
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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101 <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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102 </param>
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103 <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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104 <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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105 </param>
5
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106 <param name="sep" type="select" label="Write each trajectory frame to a separate GRO or PDB file?" help="Results will be stored as a Galaxy collection. Only has effect with PDB or GRO output, otherwise ignored">
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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107 <option value="" selected="true">No</option>
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108 <option value="sep">Yes, write each frame separately</option>
0
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109 </param>
5
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110 <conditional name="pbc">
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111 <param name="pbc" type="select" label="PBC treatment">
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112 <option value="none">none</option>
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113 <option value="mol">mol</option>
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114 <option value="res">res</option>
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115 <option value="atom">atom</option>
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116 <option value="nojump">nojump</option>
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117 <option value="cluster">cluster</option>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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118 <option value="whole">whole</option>
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119 </param>
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120 <when value="cluster">
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121 <param name="index_cluster" type="text" label="Index of group to use for clustering" help="Index of group to use for clustering - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0).">
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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122 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
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123 </param>
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124 </when>
16
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125 <when value="none"/>
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126 <when value="mol"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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127 <when value="res"/>
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128 <when value="atom"/>
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129 <when value="nojump"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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130 <when value="whole"/>
5
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131 </conditional>
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132 <param name="ur" type="select" label="Unit cell representation" help="Only has effect in combination with PBC treatment of mol, res or atom">
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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133 <option value="rect" selected="true">rect</option>
1
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134 <option value="tric">tric</option>
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135 <option value="compact">compact</option>
0
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136 </param>
16
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137 <param name="skip" type="integer" min="1" value="1" label="Number of frames to skip" help="This allows you to compress a trajectory file, by reducing the amount of frames written out into the new trajectory file."/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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138 <param name="boxcenter" type="select" label="Center for PBC and centering treatment">
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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139 <option value="rect">rect</option>
1
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140 <option value="tric" selected="true">tric</option>
e9cc595562b8 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit e40a6ea54592a2c6e40e44bbad52985fcdcaddb3"
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141 <option value="zero">zero</option>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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142 </param>
5
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143 <conditional name="fit">
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144 <param name="fit" type="select" label="Fit molecule to reference structure in the reference file?">
5
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145 <option value="none" selected="true">No fitting</option>
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146 <option value="rot+trans">rot+trans</option>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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147 <option value="rotxy+transxy">rotxy+transxy</option>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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148 <option value="translation">translation</option>
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149 <option value="transxy">transxy</option>
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150 <option value="progressive">progressive</option>
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151 </param>
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152 <when value="none"/>
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153 <expand macro="fit_when" option="rot+trans"/>
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154 <expand macro="fit_when" option="rotxy+transxy"/>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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155 <expand macro="fit_when" option="translation"/>
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156 <expand macro="fit_when" option="transxy"/>
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157 <expand macro="fit_when" option="progressive"/>
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158 </conditional>
0
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159 </when>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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160 <when value="trjcat">
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161 <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 that the order of concatenation is the same as the consecutive order of these selected inputs." multiple="true"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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162 <repeat name="inputtrajs" title="Select input trajectories" min="0">
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163 <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 that the order of concatenation is the same as the consecutive order of these selected inputs." multiple="true"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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164 </repeat>
0
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165 <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/>
16
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166 <param name="sep" type="hidden" value=""/>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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167 </when>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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168 </conditional>
16
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169 <param name="output_format" type="select" label="Output format">
0
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170 <option value="xtc">XTC</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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171 <option value="trr">TRR</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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172 <option value="pdb">PDB</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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173 <option value="gro">GRO</option>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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174 </param>
16
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175 <section title="Time" name="time" expanded="true">
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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176 <param name="b" type="integer" label="Start time" help="Time (ps) of first frame to read from trajectory" value="0" min="0"/>
16
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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177 <param name="e" type="integer" label="End time" help="Time (ps) of last frame to read from trajectory" value="-1" min="-1"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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178 <!-- stupidly this has different default values for trjconv and trjcat -->
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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179 <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"/>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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180 </section>
16
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181 <expand macro="log"/>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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182 </inputs>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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183 <outputs>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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184 <data name="output" format="xtc">
5
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185 <filter>not trj.get("sep") or output_format in ["xtc", "trr"]</filter>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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186 <change_format>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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187 <when input="output_format" value="trr" format="trr"/>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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188 <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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189 <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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190 <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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191 </change_format>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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192 </data>
5
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193 <collection type="list" name="gro_frames" label="Trajectory frames">
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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194 <filter>trj.get("sep") and output_format == "gro"</filter>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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195 <discover_datasets pattern="(?P&lt;designation&gt;^output[0-9]{9}\.gro$)" ext="gro"/>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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196 </collection>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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197 <collection type="list" name="pdb_frames" label="Trajectory frames">
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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198 <filter>trj.get("sep") and output_format == 'pdb'</filter>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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199 <discover_datasets pattern="(?P&lt;designation&gt;^output[0-9]{9}\.pdb$)" ext="pdb"/>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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200 </collection>
16
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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201 <expand macro="log_outputs"/>
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202 </outputs>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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203 <tests>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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204 <test>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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205 <!-- gmx trjcat -f npt.xtc nvt.xtc -cat -o test.xtc -->
16
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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diff changeset
206 <param name="trj_op" value="trjcat"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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207 <param name="trj_input" value="npt.xtc,nvt.xtc"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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208 <param name="b" value="0"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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diff changeset
209 <param name="e" value="-1"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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210 <param name="dt" value="0"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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211 <param name="cat" value="true"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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212 <output name="output" file="trjcat.xtc" ftype="xtc"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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213 </test>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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214 <test>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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215 <!-- gmx trjcat -f npt.xtc nvt.xtc -cat -o test.xtc -->
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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216 <conditional name="trj">
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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217 <param name="trj_op" value="trjcat"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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218 <param name="trj_input" value="npt.xtc"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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219 <repeat name="inputtrajs">
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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220 <param name="trj_input" value="nvt.xtc"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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221 </repeat>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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222 <param name="cat" value="true"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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223 </conditional>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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224 <param name="output_format" value="xtc"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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225 <section name="time">
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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226 <param name="b" value="0"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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227 <param name="e" value="-1"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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228 <param name="dt" value="0"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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229 </section>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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230 <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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231 </test>
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232 <test>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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233 <!-- echo '1 1' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -o npt_c.xtc -->
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234 <!-- <param name="trj_op" value="trjconv" /> -->
16
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235 <param name="trj_input" value="npt.xtc"/>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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236 <param name="str_input" value="npt.tpr" ftype="tpr"/>
16
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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237 <param name="ndx_input" value="index.ndx"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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238 <param name="b" value="0"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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239 <param name="e" value="-1"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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240 <param name="dt" value="0"/>
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241 <param name="index_output" value="1"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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242 <param name="index_center" value="1"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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243 <param name="pbc" value="mol"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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244 <param name="ur" value="tric"/>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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245 <output name="output" file="trjconv.xtc" ftype="xtc"/>
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246 </test>
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247 <test>
16
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248 <!-- testing skip -->
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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249 <!-- echo '1 1' | gmx trjconv -f npt.xtc -s npt.tpr -n -center -pbc mol -ur compact -skip 2 -o npt_c.xtc -->
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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250 <!-- <param name="trj_op" value="trjconv" /> -->
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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251 <param name="trj_input" value="npt.xtc"/>
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252 <param name="str_input" value="npt.tpr" ftype="tpr"/>
16
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253 <param name="ndx_input" value="index.ndx"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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254 <param name="b" value="0"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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255 <param name="e" value="-1"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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256 <param name="dt" value="0"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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257 <param name="index_output" value="1"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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258 <param name="index_center" value="1"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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259 <param name="pbc" value="mol"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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260 <param name="ur" value="compact"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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261 <param name="skip" value="2"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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262 <output name="output" file="trjconv_skip2.xtc" ftype="xtc"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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263 </test>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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264 <test>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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265 <!-- test sep flag -->
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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266 <param name="trj_input" value="npt.xtc"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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267 <param name="str_input" value="npt.tpr" ftype="tpr"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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268 <param name="ndx_input" value="index.ndx"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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269 <param name="b" value="0"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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270 <param name="e" value="-1"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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271 <param name="dt" value="0"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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272 <param name="index_output" value="0"/>
32052c6c3310 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 4bffc6aa89cd0e6d6435a6e571b3836eaab076f1
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273 <param name="sep" value="sep"/>
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274 <param name="output_format" value="pdb"/>
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275 <output_collection name="pdb_frames" type="list">
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276 <element name="output000000007.pdb" ftype="pdb" file="frame7.pdb"/>
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277 </output_collection>
cdf93d057569 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
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278 </test>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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279 </tests>
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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280 <help><![CDATA[
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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281
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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282 .. class:: infomark
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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283
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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284 **What it does**
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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285
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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286 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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287
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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288 _____
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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289
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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290
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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291 .. class:: infomark
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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292
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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293 **Input**
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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294
7
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295 - One or more trajectory files (XTC or TRR)
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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296 - Structure file (optional)
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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297 - 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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298
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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299 _____
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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300
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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301
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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302 .. class:: infomark
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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303
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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304 **Output**
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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305
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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306 - 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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307
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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308
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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309 ]]></help>
16
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310 <expand macro="citations"/>
0
bb0053c4e4f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 03127e495a0a1a022928c1a03527974c9e81b5a1"
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311 </tool>