Mercurial > repos > chemteam > md_converter
comparison md_converter.xml @ 4:1c25c23ff450 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author | chemteam |
---|---|
date | Wed, 20 Nov 2019 11:16:29 -0500 |
parents | |
children | 79e8ab8f1e81 |
comparison
equal
deleted
inserted
replaced
3:d76bea4c85f3 | 4:1c25c23ff450 |
---|---|
1 <tool id="md_converter" name="MDTraj file converter" version="1.9.3.1"> | |
2 | |
3 <description>- interconvert between MD trajectory file formats.</description> | |
4 | |
5 <requirements> | |
6 <requirement type="package" version="1.9.3">mdtraj</requirement> | |
7 </requirements> | |
8 | |
9 <command detect_errors="exit_code"><![CDATA[ | |
10 | |
11 ln -s '$input_file' ./input.$input_file.ext && | |
12 mdconvert ./input.$input_file.ext -o ./output.${output_format} && | |
13 cp ./output.${output_format} $output | |
14 | |
15 ]]></command> | |
16 <inputs> | |
17 <param argument="input_file" type="data" format='xtc, trr, dcd' label="Input file for conversion"/> | |
18 <param argument="output_format" type="select" label="Output format"> | |
19 <option value="trr">TRR file</option> | |
20 <option value="xtc">XTC file</option> | |
21 <option value="dcd">DCD file</option> | |
22 </param> | |
23 </inputs> | |
24 | |
25 <outputs> | |
26 <data name="output"> | |
27 <change_format> | |
28 <when input="output_format" value="trr" format="trr"/> | |
29 <when input="output_format" value="xtc" format="xtc"/> | |
30 <when input="output_format" value="dcd" format="dcd"/> | |
31 </change_format> | |
32 </data> | |
33 </outputs> | |
34 | |
35 <tests> | |
36 <test> | |
37 <param name="conversion" value="traj" /> | |
38 <param name="output_format" value="dcd" /> | |
39 <param name="input_file" value="traj.xtc" ftype="xtc"/> | |
40 <output name="output" file="traj.dcd" compare="sim_size"/> | |
41 </test> | |
42 <test> | |
43 <param name="conversion" value="traj" /> | |
44 <param name="output_format" value="trr" /> | |
45 <param name="input_file" value="traj.dcd" ftype="dcd"/> | |
46 <output name="output" file="traj.trr"/> | |
47 </test> | |
48 </tests> | |
49 <help><![CDATA[ | |
50 **What it does** | |
51 | |
52 This tool interconverts between MD trajectory file formats: xtc, trr and dcd. | |
53 | |
54 _____ | |
55 | |
56 | |
57 .. class:: infomark | |
58 | |
59 **Input** | |
60 | |
61 - Trajectory file (trr, xtc, dcd) | |
62 | |
63 _____ | |
64 | |
65 | |
66 .. class:: infomark | |
67 | |
68 **Output** | |
69 | |
70 - Trajectory file (trr, xtc, dcd) | |
71 ]]></help> | |
72 <citations> | |
73 <citation type="doi">10.1016/j.bpj.2015.08.015</citation> | |
74 </citations> | |
75 </tool> |