Mercurial > repos > chemteam > md_converter
annotate md_converter.xml @ 5:56ef0cdb8e86 draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
| author | chemteam |
|---|---|
| date | Mon, 24 Feb 2020 18:46:28 +0000 |
| parents | ec3c691f20c2 |
| children |
| rev | line source |
|---|---|
|
5
56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
chemteam
parents:
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1 <tool id="md_converter" name="MDTraj file converter" version="1.9.3.2"> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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2 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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3 <description>- interconvert between MD trajectory file formats.</description> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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4 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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5 <requirements> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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6 <requirement type="package" version="1.9.3">mdtraj</requirement> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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7 </requirements> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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8 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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9 <command detect_errors="exit_code"><![CDATA[ |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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10 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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11 ln -s '$input_file' ./input.$input_file.ext && |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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12 mdconvert ./input.$input_file.ext -o ./output.${output_format} && |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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13 cp ./output.${output_format} $output |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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14 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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15 ]]></command> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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16 <inputs> |
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5
56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
chemteam
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17 <param argument="input_file" type="data" format='xtc,trr,dcd,netcdf' label="Input file for conversion"/> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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18 <param argument="output_format" type="select" label="Output format"> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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19 <option value="trr">TRR file</option> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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20 <option value="xtc">XTC file</option> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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21 <option value="dcd">DCD file</option> |
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5
56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
chemteam
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22 <option value="netcdf">NETCDF file</option> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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23 </param> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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24 </inputs> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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25 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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26 <outputs> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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27 <data name="output"> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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28 <change_format> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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29 <when input="output_format" value="trr" format="trr"/> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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30 <when input="output_format" value="xtc" format="xtc"/> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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31 <when input="output_format" value="dcd" format="dcd"/> |
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5
56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
chemteam
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32 <when input="output_format" value="netcdf" format="netcdf"/> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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33 </change_format> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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34 </data> |
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5
56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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35 </outputs> |
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4
ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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36 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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37 <tests> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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38 <test> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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39 <param name="conversion" value="traj" /> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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40 <param name="output_format" value="dcd" /> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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41 <param name="input_file" value="traj.xtc" ftype="xtc"/> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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42 <output name="output" file="traj.dcd" compare="sim_size"/> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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43 </test> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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44 <test> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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45 <param name="conversion" value="traj" /> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
parents:
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46 <param name="output_format" value="trr" /> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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47 <param name="input_file" value="traj.dcd" ftype="dcd"/> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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48 <output name="output" file="traj.trr"/> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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49 </test> |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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50 <test> |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
chemteam
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51 <param name="conversion" value="traj" /> |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
chemteam
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52 <param name="output_format" value="netcdf" /> |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
chemteam
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53 <param name="input_file" value="traj.trr" ftype="trr"/> |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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54 <output name="output"> |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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55 <assert_contents> |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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56 <has_size value="461416" delta="6000"/> |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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57 </assert_contents> |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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58 </output> |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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59 </test> |
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4
ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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60 </tests> |
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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 <help><![CDATA[ |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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62 **What it does** |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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63 |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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64 This tool interconverts between MD trajectory file formats: xtc, trr, dcd and netcdf. |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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65 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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66 _____ |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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67 |
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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 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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69 .. class:: infomark |
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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 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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71 **Input** |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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72 |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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73 - Trajectory file (trr, xtc, dcd, netcdf) |
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56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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74 |
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4
ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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75 _____ |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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76 |
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5
56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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77 |
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4
ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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78 .. class:: infomark |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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79 |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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80 **Output** |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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81 |
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5
56ef0cdb8e86
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit 3a9e92e1bcca2d2dc9b4f1bf6a4fcf94838f43f4"
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82 - Trajectory file (trr, xtc, dcd, netcdf) |
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4
ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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83 ]]></help> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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84 <citations> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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85 <citation type="doi">10.1016/j.bpj.2015.08.015</citation> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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86 </citations> |
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ec3c691f20c2
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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87 </tool> |