Mercurial > repos > chemteam > md_converter
annotate md_converter.xml @ 9:ba83f0923369 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
author | chemteam |
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date | Wed, 14 Jul 2021 11:15:09 +0000 |
parents | |
children | be3cb628aa3e |
rev | line source |
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9
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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1 <tool id="md_converter" name="MDTraj file converter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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2 <description>- interconvert between MD trajectory file formats.</description> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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3 <macros> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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4 <token name="@TOOL_VERSION@">1.9.6</token> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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5 <token name="@GALAXY_VERSION@">0</token> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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6 </macros> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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7 <requirements> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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8 <requirement type="package" version="@TOOL_VERSION@">mdtraj</requirement> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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9 </requirements> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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10 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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11 <command detect_errors="exit_code"><![CDATA[ |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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12 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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13 ln -s '$input_file' ./input.$input_file.ext && |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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14 mdconvert ./input.$input_file.ext -o ./output.${output_format} && |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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15 cp ./output.${output_format} $output |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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16 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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17 ]]></command> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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18 <inputs> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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19 <param argument="input_file" type="data" format='xtc,trr,dcd,netcdf' label="Input file for conversion"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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20 <param argument="output_format" type="select" label="Output format"> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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21 <option value="trr">TRR file</option> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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22 <option value="xtc">XTC file</option> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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23 <option value="dcd">DCD file</option> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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24 <option value="netcdf">NETCDF file</option> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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25 </param> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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26 </inputs> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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27 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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28 <outputs> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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29 <data name="output"> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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30 <change_format> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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31 <when input="output_format" value="trr" format="trr"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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32 <when input="output_format" value="xtc" format="xtc"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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33 <when input="output_format" value="dcd" format="dcd"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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34 <when input="output_format" value="netcdf" format="netcdf"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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35 </change_format> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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36 </data> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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37 </outputs> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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38 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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39 <tests> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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40 <test> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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41 <param name="conversion" value="traj" /> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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42 <param name="output_format" value="dcd" /> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
parents:
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43 <param name="input_file" value="traj.xtc" ftype="xtc"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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44 <output name="output" file="traj.dcd" compare="sim_size"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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45 </test> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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46 <test> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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47 <param name="conversion" value="traj" /> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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48 <param name="output_format" value="trr" /> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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49 <param name="input_file" value="traj.dcd" ftype="dcd"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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50 <output name="output" file="traj.trr"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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51 </test> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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52 <test> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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53 <param name="conversion" value="traj" /> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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54 <param name="output_format" value="netcdf" /> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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55 <param name="input_file" value="traj.trr" ftype="trr"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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56 <output name="output"> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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57 <assert_contents> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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58 <has_size value="461416" delta="6000"/> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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59 </assert_contents> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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60 </output> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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61 </test> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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62 </tests> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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63 <help><![CDATA[ |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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64 **What it does** |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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65 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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66 This tool interconverts between MD trajectory file formats: xtc, trr, dcd and netcdf. |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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67 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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68 _____ |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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69 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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70 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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71 .. class:: infomark |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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72 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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73 **Input** |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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74 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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75 - Trajectory file (trr, xtc, dcd, netcdf) |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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76 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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77 _____ |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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78 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
chemteam
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79 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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80 .. class:: infomark |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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81 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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82 **Output** |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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83 |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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84 - Trajectory file (trr, xtc, dcd, netcdf) |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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85 ]]></help> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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86 <citations> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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87 <citation type="doi">10.1016/j.bpj.2015.08.015</citation> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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88 </citations> |
ba83f0923369
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a6a1b0dc37ce54aae5e88dba50a1b8056739f443"
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89 </tool> |