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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 1310371ed706e7cf287c848363102f8a476647de
author chemteam
date Mon, 24 Oct 2022 22:35:01 +0000
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-1:000000000000 0:f261fded9631
1 <tool id="gmx_rmsf" name="GROMACS RMSF calculation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="21.09">
2 <description>of molecular structures</description>
3 <macros>
4 <import>macros.xml</import>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9
10 ln -s '$traj_input' ./traj_input.${traj_input.ext} &&
11 ln -s '$structure_input' ./structure_input.${structure_input.ext} &&
12 #if $ndx_input:
13 ln -s '$ndx_input' ./ndx_input.${ndx_input.ext} &&
14 #end if
15 echo '$index' | gmx rmsf
16
17 ##inputs
18 -f ./traj_input.${traj_input.ext}
19 -s ./structure_input.${structure_input.ext}
20 #if $ndx_input:
21 -n ./ndx_input.${ndx_input.ext}
22 #end if
23 -xvg '$outputformat'
24
25 ## other options
26 #if $resavg == 'true':
27 -res
28 #end if
29
30 >> verbose.txt 2>&1
31
32 ]]></command>
33 <inputs>
34 <param name="traj_input" type="data" format="trr,xtc" label="Trajectory file" help="In XTC or TRR format"/>
35 <param name="structure_input" type="data" format="tpr,pdb,gro" label="Structure file" help="In TPR, PDB, or GRO format. Use a tpr file if your system contains nonstandard atom types, as atomic masses may not be directly obtained from PDB or GRO files."/>
36 <param name="ndx_input" type="data" format="ndx" optional="true" label="Index (NDX) file" help="Index file (optional) containing your system's different atomic and molecular groups. If not specified, GROMACS uses a default set of groups."/>
37 <param name="index" type="integer" value="0" min="0" label="Index of group" help="Index of group for calculating the Root Mean Square Fluctuation (RMSF) - i.e. the group's position in the ndx file (using zero-based numbering, so the first group has index 0)."/>
38 <param name="resavg" type="select" label="Calculate average RMSF for entire residues?" help="This option works best if the selected index group mainly includes whole residues.">
39 <option value="false">No</option>
40 <option value="true">Yes</option>
41 </param>
42 <param name="outputformat" type="select" label="Output format" help="The default XVG format is compatible with XMGRACE and includes all of the graph's parameters. The raw data just includes 2 columns, one for the frame index and second for the corresponding RMSF value.">
43 <option value="xmgrace" selected="true">XVG</option>
44 <option value="none">Raw Data</option>
45 </param>
46 <expand macro="log"/>
47 </inputs>
48 <outputs>
49 <data name="rmsf_output" format="xvg" from_work_dir="rmsf.xvg" label="GROMACS calculation of RMSF on ${on_string}"/>
50 <expand macro="log_outputs"/>
51 </outputs>
52 <tests>
53 <test expect_num_outputs="1">
54 <param name="traj_input" value="npt.xtc"/>
55 <param name="structure_input" value="npt.tpr" ftype="tpr"/>
56 <param name="ndx_input" value="index.ndx" ftype="ndx"/>
57 <param name="index" value="3"/>
58 <param name="outputformat" value="xmgrace"/>
59 <output name="rmsf_output" ftype="xvg">
60 <assert_contents>
61 <has_text text="5 0.0113"/>
62 <has_text text="27 0.0136"/>
63 <has_text text="43 0.0134"/>
64 </assert_contents>
65 </output>
66 </test>
67 <test expect_num_outputs="1">
68 <param name="traj_input" value="npt.xtc"/>
69 <param name="structure_input" value="npt.tpr" ftype="tpr"/>
70 <param name="ndx_input" value="index.ndx" ftype="ndx"/>
71 <param name="index" value="1"/>
72 <param name="resavg" value="true"/>
73 <param name="outputformat" value="none"/>
74 <output name="rmsf_output" ftype="xvg">
75 <assert_contents>
76 <has_text text="1 0.0263"/>
77 <has_text text="2 0.0230"/>
78 <has_text text="3 0.0201"/>
79 </assert_contents>
80 </output>
81 </test>
82 <!-- test without optional ndx -->
83 <test expect_num_outputs="1">
84 <param name="traj_input" value="npt.xtc"/>
85 <param name="structure_input" value="npt.tpr" ftype="tpr"/>
86 <param name="index" value="1"/>
87 <param name="resavg" value="true"/>
88 <param name="outputformat" value="none"/>
89 <output name="rmsf_output" ftype="xvg">
90 <assert_contents>
91 <has_text text="1 0.0263"/>
92 <has_text text="2 0.0230"/>
93 <has_text text="3 0.0201"/>
94 </assert_contents>
95 </output>
96 </test>
97 </tests>
98 <help><![CDATA[
99
100 .. class:: infomark
101
102 **What it does**
103
104 This tool calculates a structure's Root Mean Square Fluctuation (RMSF), using GROMACS.
105
106 _____
107
108 .. class:: infomark
109
110 **Input**
111
112 - GRO, PDB, or TPR structure file.
113 - TRR or XTC trajectory file.
114
115
116 _____
117
118
119 .. class:: infomark
120
121 **Output**
122
123 - XVG file containing RMSF results.
124
125 ]]></help>
126 <expand macro="citations"/>
127 </tool>