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comparison md_slicer.xml @ 6:795e3abe95f0 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4fbd1b2fbe605c810b323de60f546b8d3f8b4b21"
author chemteam
date Thu, 11 Mar 2021 19:51:33 +0000
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5:79e8ab8f1e81 6:795e3abe95f0
1 <tool id="md_slicer" name="Slice MD trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>using the MDTraj package</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.9.5</token>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">mdtraj</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 ln -s '$traj' traj.${traj.ext} &&
12 mdconvert traj.${traj.ext} -o output.${traj.ext} -i $start:$end:$stride &&
13 mv output.${traj.ext} '$output'
14 ]]></command>
15 <inputs>
16 <param argument="traj" type="data" format='xtc,dcd' label="Input trajectory file for slicing"/>
17 <param argument="start" type="integer" value="0" label="Start frame for slicing"/>
18 <param argument="end" type="integer" value="10000" label="End frame for slicing"/>
19 <param argument="stride" type="integer" value="1" label="Stride" help="i.e. load every nth frame from the input file"/>
20 </inputs>
21 <outputs>
22 <data name="output" format_source="traj"/>
23 </outputs>
24 <tests>
25 <test>
26 <param name="traj" value="traj.xtc" />
27 <param name="start" value="0" />
28 <param name="end" value="8" />
29 <param name="stride" value="2" />
30 <output name="output" file="traj_slice.xtc" />
31 </test>
32 <test>
33 <param name="traj" value="traj.dcd" />
34 <param name="start" value="1" />
35 <param name="end" value="6" />
36 <param name="stride" value="1" />
37 <output name="output" file="traj_slice.dcd" compare="sim_size"/>
38 </test>
39 </tests>
40 <help><![CDATA[
41 **What it does**
42
43 This tool extracts a segment from a molecular dynamcics trajectory (i.e. performs a slice).
44
45 _____
46
47
48 .. class:: infomark
49
50 **Input**
51
52 - Trajectory file (xtc, dcd)
53
54 In addition, a start frame and end frame have to be specified for the output trajectory,
55 as well as a value for the 'stride' (to save only every nth frame in the output file).
56 _____
57
58
59 .. class:: infomark
60
61 **Output**
62
63 - Trajectory file (xtc, dcd) extracted from the input file.
64 ]]></help>
65 <citations>
66 <citation type="doi">10.1016/j.bpj.2015.08.015</citation>
67 </citations>
68 </tool>