Mercurial > repos > chemteam > md_converter
comparison md_converter.xml @ 5:79e8ab8f1e81 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
author | chemteam |
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date | Mon, 24 Feb 2020 13:46:47 -0500 |
parents | 1c25c23ff450 |
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4:1c25c23ff450 | 5:79e8ab8f1e81 |
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1 <tool id="md_converter" name="MDTraj file converter" version="1.9.3.1"> | 1 <tool id="md_converter" name="MDTraj file converter" version="1.9.3.2"> |
2 | 2 |
3 <description>- interconvert between MD trajectory file formats.</description> | 3 <description>- interconvert between MD trajectory file formats.</description> |
4 | 4 |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="1.9.3">mdtraj</requirement> | 6 <requirement type="package" version="1.9.3">mdtraj</requirement> |
12 mdconvert ./input.$input_file.ext -o ./output.${output_format} && | 12 mdconvert ./input.$input_file.ext -o ./output.${output_format} && |
13 cp ./output.${output_format} $output | 13 cp ./output.${output_format} $output |
14 | 14 |
15 ]]></command> | 15 ]]></command> |
16 <inputs> | 16 <inputs> |
17 <param argument="input_file" type="data" format='xtc, trr, dcd' label="Input file for conversion"/> | 17 <param argument="input_file" type="data" format='xtc,trr,dcd,netcdf' label="Input file for conversion"/> |
18 <param argument="output_format" type="select" label="Output format"> | 18 <param argument="output_format" type="select" label="Output format"> |
19 <option value="trr">TRR file</option> | 19 <option value="trr">TRR file</option> |
20 <option value="xtc">XTC file</option> | 20 <option value="xtc">XTC file</option> |
21 <option value="dcd">DCD file</option> | 21 <option value="dcd">DCD file</option> |
22 <option value="netcdf">NETCDF file</option> | |
22 </param> | 23 </param> |
23 </inputs> | 24 </inputs> |
24 | 25 |
25 <outputs> | 26 <outputs> |
26 <data name="output"> | 27 <data name="output"> |
27 <change_format> | 28 <change_format> |
28 <when input="output_format" value="trr" format="trr"/> | 29 <when input="output_format" value="trr" format="trr"/> |
29 <when input="output_format" value="xtc" format="xtc"/> | 30 <when input="output_format" value="xtc" format="xtc"/> |
30 <when input="output_format" value="dcd" format="dcd"/> | 31 <when input="output_format" value="dcd" format="dcd"/> |
32 <when input="output_format" value="netcdf" format="netcdf"/> | |
31 </change_format> | 33 </change_format> |
32 </data> | 34 </data> |
33 </outputs> | 35 </outputs> |
34 | 36 |
35 <tests> | 37 <tests> |
36 <test> | 38 <test> |
37 <param name="conversion" value="traj" /> | 39 <param name="conversion" value="traj" /> |
38 <param name="output_format" value="dcd" /> | 40 <param name="output_format" value="dcd" /> |
43 <param name="conversion" value="traj" /> | 45 <param name="conversion" value="traj" /> |
44 <param name="output_format" value="trr" /> | 46 <param name="output_format" value="trr" /> |
45 <param name="input_file" value="traj.dcd" ftype="dcd"/> | 47 <param name="input_file" value="traj.dcd" ftype="dcd"/> |
46 <output name="output" file="traj.trr"/> | 48 <output name="output" file="traj.trr"/> |
47 </test> | 49 </test> |
50 <test> | |
51 <param name="conversion" value="traj" /> | |
52 <param name="output_format" value="netcdf" /> | |
53 <param name="input_file" value="traj.trr" ftype="trr"/> | |
54 <output name="output"> | |
55 <assert_contents> | |
56 <has_size value="461416" delta="6000"/> | |
57 </assert_contents> | |
58 </output> | |
59 </test> | |
48 </tests> | 60 </tests> |
49 <help><![CDATA[ | 61 <help><![CDATA[ |
50 **What it does** | 62 **What it does** |
51 | 63 |
52 This tool interconverts between MD trajectory file formats: xtc, trr and dcd. | 64 This tool interconverts between MD trajectory file formats: xtc, trr, dcd and netcdf. |
53 | 65 |
54 _____ | 66 _____ |
55 | 67 |
56 | 68 |
57 .. class:: infomark | 69 .. class:: infomark |
58 | 70 |
59 **Input** | 71 **Input** |
60 | 72 |
61 - Trajectory file (trr, xtc, dcd) | 73 - Trajectory file (trr, xtc, dcd, netcdf) |
62 | 74 |
63 _____ | 75 _____ |
64 | 76 |
65 | 77 |
66 .. class:: infomark | 78 .. class:: infomark |
67 | 79 |
68 **Output** | 80 **Output** |
69 | 81 |
70 - Trajectory file (trr, xtc, dcd) | 82 - Trajectory file (trr, xtc, dcd, netcdf) |
71 ]]></help> | 83 ]]></help> |
72 <citations> | 84 <citations> |
73 <citation type="doi">10.1016/j.bpj.2015.08.015</citation> | 85 <citation type="doi">10.1016/j.bpj.2015.08.015</citation> |
74 </citations> | 86 </citations> |
75 </tool> | 87 </tool> |