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