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annotate md_slicer.xml @ 8:730ef07b90ae draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
author chemteam
date Thu, 24 Jun 2021 21:09:24 +0000
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730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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1 <tool id="md_slicer" name="Slice MD trajectories" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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2 <description>using the MDTraj package</description>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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3 <macros>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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4 <token name="@TOOL_VERSION@">1.9.6</token>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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5 <token name="@GALAXY_VERSION@">0</token>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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6 </macros>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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7 <requirements>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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8 <requirement type="package" version="@TOOL_VERSION@">mdtraj</requirement>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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9 </requirements>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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10 <command detect_errors="exit_code"><![CDATA[
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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11 ln -s '$traj' traj.${traj.ext} &&
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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12 mdconvert traj.${traj.ext} -o output.${traj.ext} -i $start:$end:$stride &&
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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13 mv output.${traj.ext} '$output'
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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14 ]]></command>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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15 <inputs>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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16 <param argument="traj" type="data" format='xtc,dcd' label="Input trajectory file for slicing"/>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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17 <param argument="start" type="integer" value="0" label="Start frame for slicing"/>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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18 <param argument="end" type="integer" value="10000" label="End frame for slicing"/>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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19 <param argument="stride" type="integer" value="1" label="Stride" help="i.e. load every nth frame from the input file"/>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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20 </inputs>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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21 <outputs>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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22 <data name="output" format_source="traj"/>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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23 </outputs>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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24 <tests>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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25 <test>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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26 <param name="traj" value="traj.xtc" />
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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27 <param name="start" value="0" />
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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28 <param name="end" value="8" />
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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29 <param name="stride" value="2" />
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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30 <output name="output" file="traj_slice.xtc" />
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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31 </test>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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32 <test>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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33 <param name="traj" value="traj.dcd" />
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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34 <param name="start" value="1" />
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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35 <param name="end" value="6" />
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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36 <param name="stride" value="1" />
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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37 <output name="output" file="traj_slice.dcd" compare="sim_size"/>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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38 </test>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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39 </tests>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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40 <help><![CDATA[
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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41 **What it does**
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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42
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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43 This tool extracts a segment from a molecular dynamcics trajectory (i.e. performs a slice).
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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44
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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45 _____
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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48 .. class:: infomark
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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49
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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50 **Input**
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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51
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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52 - Trajectory file (xtc, dcd)
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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53
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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54 In addition, a start frame and end frame have to be specified for the output trajectory,
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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55 as well as a value for the 'stride' (to save only every nth frame in the output file).
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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56 _____
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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57
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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59 .. class:: infomark
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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61 **Output**
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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62
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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63 - Trajectory file (xtc, dcd) extracted from the input file.
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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64 ]]></help>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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65 <citations>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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66 <citation type="doi">10.1016/j.bpj.2015.08.015</citation>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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67 </citations>
730ef07b90ae "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdslicer commit 4ea801b442afefb53273fb8854024358ea1dbdae"
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68 </tool>