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annotate md_converter.xml @ 4:ec3c691f20c2 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author chemteam
date Wed, 20 Nov 2019 16:09:41 +0000
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children 56ef0cdb8e86
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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1 <tool id="md_converter" name="MDTraj file converter" version="1.9.3.1">
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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3 <description>- interconvert between MD trajectory file formats.</description>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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5 <requirements>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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6 <requirement type="package" version="1.9.3">mdtraj</requirement>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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7 </requirements>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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9 <command detect_errors="exit_code"><![CDATA[
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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11 ln -s '$input_file' ./input.$input_file.ext &&
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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12 mdconvert ./input.$input_file.ext -o ./output.${output_format} &&
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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13 cp ./output.${output_format} $output
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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15 ]]></command>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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16 <inputs>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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17 <param argument="input_file" type="data" format='xtc, trr, dcd' label="Input file for conversion"/>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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18 <param argument="output_format" type="select" label="Output format">
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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19 <option value="trr">TRR file</option>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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20 <option value="xtc">XTC file</option>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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21 <option value="dcd">DCD file</option>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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22 </param>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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23 </inputs>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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25 <outputs>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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26 <data name="output">
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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27 <change_format>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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28 <when input="output_format" value="trr" format="trr"/>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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29 <when input="output_format" value="xtc" format="xtc"/>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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30 <when input="output_format" value="dcd" format="dcd"/>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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31 </change_format>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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32 </data>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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33 </outputs>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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35 <tests>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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36 <test>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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37 <param name="conversion" value="traj" />
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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38 <param name="output_format" value="dcd" />
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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39 <param name="input_file" value="traj.xtc" ftype="xtc"/>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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40 <output name="output" file="traj.dcd" compare="sim_size"/>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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41 </test>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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42 <test>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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43 <param name="conversion" value="traj" />
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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44 <param name="output_format" value="trr" />
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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45 <param name="input_file" value="traj.dcd" ftype="dcd"/>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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46 <output name="output" file="traj.trr"/>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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47 </test>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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48 </tests>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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49 <help><![CDATA[
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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50 **What it does**
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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52 This tool interconverts between MD trajectory file formats: xtc, trr and dcd.
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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54 _____
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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57 .. class:: infomark
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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59 **Input**
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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61 - Trajectory file (trr, xtc, dcd)
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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63 _____
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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66 .. class:: infomark
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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68 **Output**
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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70 - Trajectory file (trr, xtc, dcd)
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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71 ]]></help>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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72 <citations>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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73 <citation type="doi">10.1016/j.bpj.2015.08.015</citation>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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74 </citations>
ec3c691f20c2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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75 </tool>