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comparison md_converter.xml @ 5:79e8ab8f1e81 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
author chemteam
date Mon, 24 Feb 2020 13:46:47 -0500
parents 1c25c23ff450
children
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4:1c25c23ff450 5:79e8ab8f1e81
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>