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comparison gyrate.xml @ 0:a5afe283962d draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 0941b05e72c90bcf5521efa52767390864be5033"
author chemteam
date Wed, 01 Dec 2021 15:34:01 +0000
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-1:000000000000 0:a5afe283962d
1 <tool id="gmx_rg" name="GROMACS Radius of Gyration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>of a molecular structure</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7
8 <expand macro="requirements" />
9 <command detect_errors="exit_code"><![CDATA[
10
11 ln -s '$traj_input' ./traj_input.${traj_input.ext} &&
12 ln -s '$structure_input' ./structure_input.${structure_input.ext} &&
13 ln -s '$ndx_input' ./ndx_input.ndx &&
14
15 echo '$index' | gmx gyrate -f './traj_input.${traj_input.ext}' -s './structure_input.${structure_input.ext}' -n './ndx_input.ndx' -o rg.xvg
16
17 >> verbose.txt 2>&1
18 #if $fmt == 'tabular':
19 &&
20 grep '@\|#' rg.xvg &&
21 grep -v '@\|#' rg.xvg | sed 's/[[:space:]]*//' | sed 's/ /\t/g' > rg.tabular
22 #end if
23
24 ]]></command>
25
26 <inputs>
27 <param name="traj_input" type="data" format='trr,xtc' label="Trajectory file" help="In XTC or TRR format"/>
28 <param name="structure_input" type="data" format='tpr' label="Structure file" help="In TPR format"/>
29 <param name="ndx_input" type="data" format='ndx' label="Index (NDX) file" help="Index file containing the molecules of interest"/>
30 <param name="index" type="text" label="Index of group" help="Index of group for calculating the radius of gyration - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0)." />
31 <expand macro="xvg_or_tab" />
32 <expand macro="log" />
33 </inputs>
34 <outputs>
35 <expand macro="xvg_or_tab_outputs" name="rg" label="Radius of Gyration on ${on_string}" />
36 <expand macro="log_outputs" />
37 </outputs>
38 <tests>
39 <test>
40 <param name="traj_input" value="npt.xtc" />
41 <param name="structure_input" value="npt.tpr" />
42 <param name="ndx_input" value="index.ndx" />
43 <param name="index" value="1" />
44 <param name="fmt" value="xvg" />
45 <output name="output1" ftype="xvg">
46 <!-- file is big, thus we do not compare the whole file -->
47 <assert_contents>
48 <has_text text=" 0 0.605945 0.570801 0.439308 0.464255"/>
49 <has_text text="0.1 0.603599 0.568297 0.439052 0.461449"/>
50 <has_text text="0.2 0.608461 0.574886 0.442389 0.46287"/>
51 <has_text text="0.3 0.605338 0.572752 0.438534 0.46099"/>
52 </assert_contents>
53 </output>
54 </test>
55 </tests>
56 <help><![CDATA[
57
58 .. class:: infomark
59
60 **What it does**
61
62 This tool computes the radius of gyration of a molecular structure, which provides an idea of how compact versus how open or extended the molecule's most commonly adopted conformation is, and how it changes throughout a trajectory. It can often be determined experimentally, so computing this from a simulation and comparing the results can also allow the researcher to verify the accuracy of the chosen force field for that particular system.
63
64 _____
65
66 .. class:: infomark
67
68 **Input**
69
70 - TPR file of the simulated system.
71 - XTC or TRR trajectory file from a prior simulation.
72 - Index file generated using the 'Create GROMACS index files' tool (make_ndx).
73
74 _____
75
76
77 .. class:: infomark
78
79 **Output**
80
81 - XVG file containing the radius of gyration at every frame of the trajectory.
82 ]]></help>
83
84 <expand macro="citations" />
85 </tool>
86