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comparison md_converter.xml @ 0:acce5039ece7 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 8aeaf3f199cccb1bbb26a29628e7bb75abaf189d
author chemteam
date Sun, 14 Oct 2018 05:31:36 -0400
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children f40eb1f8536f
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1 <tool id="md_converter" name="MDTraj file converter" version="1.9.1">
2
3 <description>- interconvert between MD trajectory or structure file formats.</description>
4
5 <requirements>
6 <requirement type="package" version="1.9.1">mdtraj</requirement>
7 <requirement type="package" version="2018.2">gromacs</requirement>
8 </requirements>
9
10 <command detect_errors="exit_code"><![CDATA[
11
12 #if $input.conversion == 'str':
13 ln -s '$input_file' ./input.$input_file.ext &&
14 gmx editconf -f ./input.$input_file.ext -o ./output.${input.output_format} &&
15 cp ./output.${input.output_format} $output
16 #end if
17
18 #if $input.conversion == 'traj':
19 ln -s '$input_file' ./input.$input_file.ext &&
20 mdconvert ./input.$input_file.ext -o ./output.${input.output_format} &&
21 cp ./output.${input.output_format} $output
22
23 #end if
24
25 ]]></command>
26 <inputs>
27 <conditional name="input">
28 <param argument="conversion" type="select" label="Type of conversion">
29 <option value="traj">Trajectory file</option>
30 <option value="str">Structure file</option>
31 </param>
32 <when value="traj">
33 <param argument="input_file" type="data" format='xtc, trr, dcd' label="Input file for conversion"/>
34 <param argument="output_format" type="select" label="Output format">
35 <option value="trr">TRR file</option>
36 <option value="xtc">XTC file</option>
37 <option value="dcd">DCD file</option>
38 </param>
39 </when>
40 <when value="str">
41 <param argument="input_file" type="data" format='gro, pdb' label="Input file for conversion"/>
42 <param argument="output_format" type="select" label="Output format">
43 <option value="gro">GRO file</option>
44 <option value="pdb">PDB file</option>
45 </param>
46 </when>
47 </conditional>
48 </inputs>
49
50 <outputs>
51 <data name="output" format="text">
52 <change_format>
53 <when input="output_format" value="gro" format="gro"/>
54 <when input="output_format" value="pdb" format="pdb"/>
55 <when input="output_format" value="trr" format="trr"/>
56 <when input="output_format" value="xtc" format="xtc"/>
57 <when input="output_format" value="dcd" format="dcd"/>
58 </change_format>
59 </data>
60 </outputs>
61
62 <tests>
63 <test>
64 <param name="conversion" value="traj" />
65 <param name="output_format" value="dcd" />
66 <param name="input_file" value="traj.xtc" />
67 <output name="output" file="traj.dcd" compare="sim_size"/>
68 </test>
69 <test>
70 <param name="conversion" value="traj" />
71 <param name="output_format" value="trr" />
72 <param name="input_file" value="traj.dcd" />
73 <output name="output" file="traj.trr"/>
74 </test>
75 <test>
76 <param name="conversion" value="str" />
77 <param name="output_format" value="gro" />
78 <param name="input_file" value="str.pdb" ftype="pdb"/>
79 <output name="output" file="str.gro" compare="sim_size"/>
80 </test>
81 <test>
82 <param name="conversion" value="str" />
83 <param name="output_format" value="pdb" />
84 <param name="input_file" value="str.gro" ftype="gro"/>
85 <output name="output" file="str2.pdb" compare="sim_size"/>
86 </test>
87 </tests>
88 <help><![CDATA[
89 **What it does**
90
91 This tool interconverts between MD file formats: xtc, trr and dcd (trajectory formats) and pdb and gro (structure formats).
92
93 _____
94
95
96 .. class:: infomark
97
98 **Input**
99
100 - Trajectory file (trr, xtc, dcd) or structure file (pdb, gro)
101
102 _____
103
104
105 .. class:: infomark
106
107 **Output**
108
109 - Trajectory file (trr, xtc, dcd) or structure file (pdb, gro)
110 ]]></help>
111 <citations>
112 <citation type="doi">10.1016/j.bpj.2015.08.015</citation>
113 <citation type="doi">10.1016/j.softx.2015.06.001</citation>
114 </citations>
115 </tool>