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comparison trj.xml @ 14:72459c3ea5f6 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 033779f5ae0fa964ccad44104027d1d715b8e907"
author chemteam
date Wed, 13 Apr 2022 19:47:07 +0000
parents 16fad30d566a
children 32052c6c3310
comparison
equal deleted inserted replaced
13:0f2ced72d16f 14:72459c3ea5f6
1 <tool id="gmx_trj" name="Modify/convert GROMACS trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> 1 <tool id="gmx_trj" name="Modify/convert GROMACS trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>using trjconv and trjcat</description> 2 <description>using trjconv and trjcat</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token> 5 <token name="@GALAXY_VERSION@">1</token>
6 <xml name="fit_when" token_option="none"> 6 <xml name="fit_when" token_option="none">
7 <when value="@OPTION@"> 7 <when value="@OPTION@">
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)."> 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).">
9 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator> 9 <validator type="regex" message="Only numeric values allowed">^[0-9]*$</validator>
10 </param> 10 </param>
16 16
17 <command detect_errors="exit_code"><![CDATA[ 17 <command detect_errors="exit_code"><![CDATA[
18 #if $trj.trj_op == 'trjcat': 18 #if $trj.trj_op == 'trjcat':
19 mkdir trajs && 19 mkdir trajs &&
20 #for $value, $file in enumerate($trj_input): 20 #for $value, $file in enumerate($trj_input):
21 ln -s '$file' trajs/traj_${value}.${file.ext} && 21 ln -s '$file' trajs/traj_${str(value).rjust(10, '0')}.${file.ext} &&
22 #end for 22 #end for
23 23
24 gmx trjcat 24 gmx trjcat
25 -f trajs/traj* ## here we assume that they all have the same ext, probably reasonable 25 -f trajs/traj* ## here we assume that they all have the same ext, probably reasonable
26 $trj.cat 26 $trj.cat
29 #elif $trj.trj_op == 'trjconv': 29 #elif $trj.trj_op == 'trjconv':
30 ln -s '$ndx_input' ./index.ndx && 30 ln -s '$ndx_input' ./index.ndx &&
31 ln -s '$str_input' ./str.${str_input.ext} && 31 ln -s '$str_input' ./str.${str_input.ext} &&
32 ln -s '$trj_input' ./traj.${trj_input.ext} && 32 ln -s '$trj_input' ./traj.${trj_input.ext} &&
33 33
34 echo ## optionally pipe in the following 34 echo ## optionally pipe in the following
35 #if $trj.fit.fit != 'none': 35 #if $trj.fit.fit != 'none':
36 '$trj.fit.index_fit' 36 '$trj.fit.index_fit'
37 #end if 37 #end if
38 #if $trj.pbc.pbc == 'cluster': 38 #if $trj.pbc.pbc == 'cluster':
39 '$trj.pbc.index_cluster' 39 '$trj.pbc.index_cluster'
40 #end if 40 #end if
41 '$trj.index_center' '$trj.index_output' | gmx trjconv 41 '$trj.index_center' '$trj.index_output' | gmx trjconv
42 -f ./traj.${trj_input.ext} 42 -f ./traj.${trj_input.ext}
43 -s ./str.${str_input.ext} 43 -s ./str.${str_input.ext}
44 #if $ndx_input: 44 #if $ndx_input:
45 -n ./index.ndx 45 -n ./index.ndx
46 #end if 46 #end if
138 <expand macro="fit_when" option="transxy"/> 138 <expand macro="fit_when" option="transxy"/>
139 <expand macro="fit_when" option="progressive"/> 139 <expand macro="fit_when" option="progressive"/>
140 </conditional> 140 </conditional>
141 </when> 141 </when>
142 <when value="trjcat"> 142 <when value="trjcat">
143 <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"/> 143 <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 if you want to take order into account when concatenating, you must use a collection as input." multiple="true"/>
144 <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/> 144 <param name="cat" type="boolean" label="Do not discard double time frames" truevalue="-cat" falsevalue="-nocat"/>
145 <param name="sep" type="hidden" value="" /> 145 <param name="sep" type="hidden" value="" />
146 </when> 146 </when>
147 </conditional> 147 </conditional>
148 <param name="output_format" type="select" label="Output format" > 148 <param name="output_format" type="select" label="Output format" >