Mercurial > repos > chemteam > md_converter
annotate md_converter.xml @ 4:1c25c23ff450 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author | chemteam |
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date | Wed, 20 Nov 2019 11:16:29 -0500 |
parents | |
children | 79e8ab8f1e81 |
rev | line source |
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4
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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1 <tool id="md_converter" name="MDTraj file converter" version="1.9.3.1"> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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2 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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3 <description>- interconvert between MD trajectory file formats.</description> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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4 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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5 <requirements> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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6 <requirement type="package" version="1.9.3">mdtraj</requirement> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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7 </requirements> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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8 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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9 <command detect_errors="exit_code"><![CDATA[ |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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10 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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11 ln -s '$input_file' ./input.$input_file.ext && |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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12 mdconvert ./input.$input_file.ext -o ./output.${output_format} && |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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13 cp ./output.${output_format} $output |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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14 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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15 ]]></command> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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16 <inputs> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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17 <param argument="input_file" type="data" format='xtc, trr, dcd' label="Input file for conversion"/> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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18 <param argument="output_format" type="select" label="Output format"> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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19 <option value="trr">TRR file</option> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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20 <option value="xtc">XTC file</option> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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21 <option value="dcd">DCD file</option> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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22 </param> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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23 </inputs> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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24 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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25 <outputs> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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26 <data name="output"> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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27 <change_format> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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28 <when input="output_format" value="trr" format="trr"/> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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29 <when input="output_format" value="xtc" format="xtc"/> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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30 <when input="output_format" value="dcd" format="dcd"/> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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31 </change_format> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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32 </data> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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33 </outputs> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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34 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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35 <tests> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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36 <test> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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37 <param name="conversion" value="traj" /> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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38 <param name="output_format" value="dcd" /> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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39 <param name="input_file" value="traj.xtc" ftype="xtc"/> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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40 <output name="output" file="traj.dcd" compare="sim_size"/> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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41 </test> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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42 <test> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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43 <param name="conversion" value="traj" /> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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44 <param name="output_format" value="trr" /> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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45 <param name="input_file" value="traj.dcd" ftype="dcd"/> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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46 <output name="output" file="traj.trr"/> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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47 </test> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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48 </tests> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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49 <help><![CDATA[ |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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50 **What it does** |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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51 |
1c25c23ff450
"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. |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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53 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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54 _____ |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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55 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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56 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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57 .. class:: infomark |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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58 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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59 **Input** |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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60 |
1c25c23ff450
"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) |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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62 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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63 _____ |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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64 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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65 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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66 .. class:: infomark |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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67 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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68 **Output** |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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69 |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
chemteam
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70 - Trajectory file (trr, xtc, dcd) |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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71 ]]></help> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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72 <citations> |
1c25c23ff450
"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> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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74 </citations> |
1c25c23ff450
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/mdfileconverter commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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75 </tool> |