Mercurial > repos > chemteam > mdanalysis_angle

annotate angle.xml @ 1:4759026f6ff4 draft

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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 9b44a37fc1a0c338693f54eaf52b582439ca9f0c
author chemteam
date Thu, 20 Dec 2018 06:49:33 -0500
parents fc7293c6cb6a
children 4c93f7541218
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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1 <tool id="mdanalysis_angle" name="Angle Analysis" version="@VERSION@">
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2 <description>Time series of Angles</description>
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3 <macros>
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4 <import>macros.xml</import>
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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 '$__tool_directory__/angle.py'
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10 --idcd '$dcdin'
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11 --ipdb '$pdbin'
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12 --isegid1 '$segid1'
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13 --iresid1 '$resid1'
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14 --iname1 '$name1'
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15 --isegid2 '$segid2'
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16 --iresid2 '$resid2'
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17 --iname2 '$name2'
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18 --isegid3 '$segid3'
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19 --iresid3 '$resid3'
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20 --iname3 '$name3'
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21 --output '$output'
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22 --oangle_plot '$angle_plot'
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23 2>&1
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24 ]]></command>
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25 <inputs>
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26 <expand macro="analysis_inputs"/>
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27 <param name="segid1" type="text" value="PRO" label="Segid of atom 1"/>
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28 <param name="resid1" type="text" value="212" label="Resid of atom 1"/>
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29 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
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30 <param name="segid2" type="text" value="HET" label="Segid of atom 2"/>
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31 <param name="resid2" type="text" value="3" label="Resid of atom 2"/>
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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32 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
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33 <param name="segid3" type="text" value="HET" label="Segid of atom 3"/>
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34 <param name="resid3" type="text" value="3" label="Resid of atom 3"/>
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35 <param name="name3" type="text" value="C2" label="Atom name of atom 3"/>
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36 </inputs>
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37 <outputs>
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38 <data format="tabular" name="output" label="Angle Analysis raw data"/>
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39 <data format="png" name="angle_plot" label="Angle Analysis Plot"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <expand macro="tests_inputs"/>
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44 <param name="segid1" value="PRO"/>
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45 <param name="resid1" value="212"/>
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46 <param name="name1" value="OE2"/>
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47 <param name="segid2" value="HET"/>
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48 <param name="resid2" value="3"/>
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49 <param name="name2" value="C1"/>
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50 <param name="segid3" value="HET"/>
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51 <param name="resid3" value="3"/>
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52 <param name="name3" value="C2"/>
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53 <output name="output">
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54 <assert_contents>
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55 <has_n_columns n="2" />
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 .. class:: infomark
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62
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63 **What it does**
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64
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65 This tool calculates and plot angle between three atoms.
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66
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67 _____
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68
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69
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70 .. class:: infomark
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71
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72 **Input**
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73
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74 - Trajectory file (DCD).
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75 - PDB file.
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76 - Segids, resids and names of the three atoms to calculate angles.
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77
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78 _____
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79
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80
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81 .. class:: infomark
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82
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83 **Output**
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84
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85 - Tab-separated file of raw data of angle between three atoms calculated for each frame.
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86 - Image (as png) of the time series graph.
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87
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88
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89 ]]></help>
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90 <expand macro="citations" />
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91 </tool>