Mercurial > repos > chemteam > mdanalysis_dihedral

annotate dihedrals.xml @ 2:2fff8653412f draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 8e1fece3eaef36823e90f5d10f8bb8b809544c55
author chemteam
date Sun, 13 Jan 2019 03:23:55 -0500
parents f95d4348ed7c
children d8178fe9aaff
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f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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1 <tool id="mdanalysis_dihedral" name="Dihedral Analysis" version="@VERSION@">
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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2 <description>Time series of dihedrals</description>
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3 <macros>
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4 <import>macros.xml</import>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 python '$__tool_directory__/dihedrals.py'
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10 --idcd '$dcdin'
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11 --ipdb '$pdbin'
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12 --isegid1 '$segid1'
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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13 --iresid1 '$resid1'
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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14 --iname1 '$name1'
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15 --isegid2 '$segid2'
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16 --iresid2 '$resid2'
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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17 --iname2 '$name2'
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18 --isegid3 '$segid3'
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19 --iresid3 '$resid3'
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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20 --iname3 '$name3'
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21 --isegid4 '$segid4'
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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22 --iresid4 '$resid4'
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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23 --iname4 '$name4'
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24 --output '$output'
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25 --odihedral_plot '$dihedral_plot'
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26 2>&1
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27 ]]></command>
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28 <inputs>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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29 <expand macro="analysis_inputs"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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30 <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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31 <param name="resid1" type="text" value="212" label="Resid of atom 1"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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32 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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33 <param name="segid2" type="text" value="HET" label="Segid of atom 2"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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34 <param name="resid2" type="text" value="3" label="Resid of atom 2"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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35 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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36 <param name="segid3" type="text" value="HET" label="Segid of atom 3"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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37 <param name="resid3" type="text" value="3" label="Resid of atom 3"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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38 <param name="name3" type="text" value="C2" label="Atom name of atom 3"/>
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39 <param name="segid4" type="text" value="HET" label="Segid of atom 4"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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40 <param name="resid4" type="text" value="3" label="Resid of atom 4"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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41 <param name="name4" type="text" value="C3" label="Atom name of atom 4"/>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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42 </inputs>
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43 <outputs>
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44 <data format="tabular" name="output" label="Dihedral analysis raw data"/>
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45 <data format="png" name="dihedral_plot" label="Dihedral Analysis Plot"/>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <expand macro="tests_inputs"/>
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50 <param name="segid1" value="PRO"/>
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51 <param name="resid1" value="212"/>
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52 <param name="name1" value="OE2"/>
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53 <param name="segid2" value="HET"/>
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54 <param name="resid2" value="3"/>
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55 <param name="name2" value="C1"/>
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56 <param name="segid3" value="HET"/>
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57 <param name="resid3" value="3"/>
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58 <param name="name3" value="C2"/>
2
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59 <param name="segid4" value="HET"/>
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60 <param name="resid4" value="3"/>
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61 <param name="name4" value="C3"/>
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62 <output name="output" file="Dihedral_analysis_raw_data.tabular" />
0
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 .. class:: infomark
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67
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68 **What it does**
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69
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70 This tool calculates and plots dihedral angles (angle between two intersecting planes) between four atoms.
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71
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72 _____
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73
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74
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75 .. class:: infomark
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76
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77 **Input**
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78
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79 - Trajectory file (DCD).
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80 - PDB file.
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81 - Segids, resids and names of the four atoms to calculate dihedral angle.
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82
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83 _____
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84
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85
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86 .. class:: infomark
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87
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88 **Output**
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89
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90 - Tab-separated file of raw data of the dihedral angle between two intersecting planes calculated for each frame.
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91 - Image (as png) of the time series graph.
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92
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93 ]]></help>
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94 <expand macro="citations" />
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
chemteam
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95 </tool>