Mercurial > repos > chemteam > md_converter
comparison md_converter.xml @ 11:d7ec25187599 draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit e21dacffada5e1405279ac09e41119508f48f63d"
author | chemteam |
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date | Tue, 30 Nov 2021 15:30:25 +0000 |
parents | be3cb628aa3e |
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10:be3cb628aa3e | 11:d7ec25187599 |
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1 <tool id="md_converter" name="MDTraj file converter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | |
2 <description>- interconvert between MD trajectory file formats.</description> | |
3 <macros> | |
4 <token name="@TOOL_VERSION@">1.9.7</token> | |
5 <token name="@GALAXY_VERSION@">0</token> | |
6 </macros> | |
7 <requirements> | |
8 <requirement type="package" version="@TOOL_VERSION@">mdtraj</requirement> | |
9 </requirements> | |
10 | |
11 <command detect_errors="exit_code"><![CDATA[ | |
12 | |
13 ln -s '$input_file' ./input.$input_file.ext && | |
14 mdconvert ./input.$input_file.ext -o ./output.${output_format} && | |
15 cp ./output.${output_format} $output | |
16 | |
17 ]]></command> | |
18 <inputs> | |
19 <param argument="input_file" type="data" format='xtc,trr,dcd,netcdf' label="Input file for conversion"/> | |
20 <param argument="output_format" type="select" label="Output format"> | |
21 <option value="trr">TRR file</option> | |
22 <option value="xtc">XTC file</option> | |
23 <option value="dcd">DCD file</option> | |
24 <option value="netcdf">NETCDF file</option> | |
25 </param> | |
26 </inputs> | |
27 | |
28 <outputs> | |
29 <data name="output"> | |
30 <change_format> | |
31 <when input="output_format" value="trr" format="trr"/> | |
32 <when input="output_format" value="xtc" format="xtc"/> | |
33 <when input="output_format" value="dcd" format="dcd"/> | |
34 <when input="output_format" value="netcdf" format="netcdf"/> | |
35 </change_format> | |
36 </data> | |
37 </outputs> | |
38 | |
39 <tests> | |
40 <test> | |
41 <param name="conversion" value="traj" /> | |
42 <param name="output_format" value="dcd" /> | |
43 <param name="input_file" value="traj.xtc" ftype="xtc"/> | |
44 <output name="output" file="traj.dcd" compare="sim_size"/> | |
45 </test> | |
46 <test> | |
47 <param name="conversion" value="traj" /> | |
48 <param name="output_format" value="trr" /> | |
49 <param name="input_file" value="traj.dcd" ftype="dcd"/> | |
50 <output name="output" file="traj.trr"/> | |
51 </test> | |
52 <test> | |
53 <param name="conversion" value="traj" /> | |
54 <param name="output_format" value="netcdf" /> | |
55 <param name="input_file" value="traj.trr" ftype="trr"/> | |
56 <output name="output"> | |
57 <assert_contents> | |
58 <has_size value="461416" delta="6000"/> | |
59 </assert_contents> | |
60 </output> | |
61 </test> | |
62 </tests> | |
63 <help><![CDATA[ | |
64 **What it does** | |
65 | |
66 This tool interconverts between MD trajectory file formats: xtc, trr, dcd and netcdf. | |
67 | |
68 _____ | |
69 | |
70 | |
71 .. class:: infomark | |
72 | |
73 **Input** | |
74 | |
75 - Trajectory file (trr, xtc, dcd, netcdf) | |
76 | |
77 _____ | |
78 | |
79 | |
80 .. class:: infomark | |
81 | |
82 **Output** | |
83 | |
84 - Trajectory file (trr, xtc, dcd, netcdf) | |
85 ]]></help> | |
86 <citations> | |
87 <citation type="doi">10.1016/j.bpj.2015.08.015</citation> | |
88 </citations> | |
89 </tool> |