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comparison md_slicer.xml @ 2:b61cbdf78765 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:53:30 -0400
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children d76bea4c85f3
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1:f40eb1f8536f 2:b61cbdf78765
1 <tool id="md_slicer" name="Slice MD trajectories" version="@VERSION@">
2 <macros>
3 <token name="@VERSION@">1.9.3</token>
4 </macros>
5 <description>using the MDTraj package</description>
6 <requirements>
7 <requirement type="package" version="@VERSION@">mdtraj</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 ln -s '$traj' traj.${traj.ext} &&
11 mdconvert traj.${traj.ext} -o output.${traj.ext} -i $start:$end:$stride &&
12 mv output.${traj.ext} '$output'
13 ]]></command>
14 <inputs>
15 <param argument="traj" type="data" format='xtc,dcd' label="Input trajectory file for slicing"/>
16 <param argument="start" type="integer" value="0" label="Start frame for slicing"/>
17 <param argument="end" type="integer" value="10000" label="End frame for slicing"/>
18 <param argument="stride" type="integer" value="1" label="Stride" help="i.e. load every nth frame from the input file"/>
19 </inputs>
20 <outputs>
21 <data name="output" format_source="traj"/>
22 </outputs>
23 <tests>
24 <test>
25 <param name="traj" value="traj.xtc" />
26 <param name="start" value="0" />
27 <param name="end" value="8" />
28 <param name="stride" value="2" />
29 <output name="output" file="traj_slice.xtc" />
30 </test>
31 <test>
32 <param name="traj" value="traj.dcd" />
33 <param name="start" value="1" />
34 <param name="end" value="6" />
35 <param name="stride" value="1" />
36 <output name="output" file="traj_slice.dcd" compare="sim_size"/>
37 </test>
38 </tests>
39 <help><![CDATA[
40 **What it does**
41
42 This tool extracts a segment from a molecular dynamcics trajectory (i.e. performs a slice).
43
44 _____
45
46
47 .. class:: infomark
48
49 **Input**
50
51 - Trajectory file (xtc, dcd)
52
53 In addition, a start frame and end frame have to be specified for the output trajectory,
54 as well as a value for the 'stride' (to save only every nth frame in the output file).
55 _____
56
57
58 .. class:: infomark
59
60 **Output**
61
62 - Trajectory file (xtc, dcd) extracted from the input file.
63 ]]></help>
64 <citations>
65 <citation type="doi">10.1016/j.bpj.2015.08.015</citation>
66 </citations>
67 </tool>