Mercurial > repos > chemteam > mdanalysis_angle

annotate angle.xml @ 4:e7d0075052c9 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:51:05 -0400
parents 4c93f7541218
children a0d210b9d287
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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 '$__tool_directory__/angle.py'
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10 --itraj '$trajin'
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11 --istr '$strin'
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12 --itrajext '$trajin.ext'
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13 --istrext '$strin.ext'
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14 --isegid1 '$segid1'
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15 --iresid1 '$resid1'
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16 --iname1 '$name1'
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17 --isegid2 '$segid2'
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18 --iresid2 '$resid2'
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19 --iname2 '$name2'
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20 --isegid3 '$segid3'
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21 --iresid3 '$resid3'
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22 --iname3 '$name3'
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23 --output '$output'
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24 --oangle_plot '$angle_plot'
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25 2>&1
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26 ]]></command>
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27 <inputs>
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28 <expand macro="analysis_inputs"/>
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29 <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/>
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30 <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/>
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31 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
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32 <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/>
e7d0075052c9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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33 <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/>
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34 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
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35 <param name="segid3" type="text" value="HET" label="Segment ID of atom 3"/>
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36 <param name="resid3" type="text" value="3" label="Residue ID of atom 3"/>
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37 <param name="name3" type="text" value="C2" label="Atom name of atom 3"/>
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38 </inputs>
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39 <outputs>
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40 <data format="tabular" name="output" label="Angle Analysis raw data"/>
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41 <data format="png" name="angle_plot" label="Angle Analysis Plot"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <expand macro="tests_inputs"/>
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46 <param name="segid1" value="PRO"/>
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47 <param name="resid1" value="212"/>
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48 <param name="name1" value="OE2"/>
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49 <param name="segid2" value="HET"/>
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50 <param name="resid2" value="3"/>
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51 <param name="name2" value="C1"/>
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52 <param name="segid3" value="HET"/>
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53 <param name="resid3" value="3"/>
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54 <param name="name3" value="C2"/>
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55 <output name="output" file="Angle_Analysis_raw_data.tabular" />
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56 </test>
4
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57 <test>
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58 <expand macro="tests_inputs_gmx"/>
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59 <param name="segid1" value="SYSTEM"/>
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60 <param name="resid1" value="212"/>
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61 <param name="name1" value="OE2"/>
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62 <param name="segid2" value="SYSTEM"/>
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63 <param name="resid2" value="3"/>
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64 <param name="name2" value="C1"/>
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65 <param name="segid3" value="SYSTEM"/>
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66 <param name="resid3" value="3"/>
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67 <param name="name3" value="C2"/>
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68 <output name="output">
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69 <assert_contents>
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70 <has_n_columns n="2" />
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71 <has_line_matching expression="0.0\t70.*" />
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72 <has_line_matching expression="10.0\t71.*" />
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73 <has_line_matching expression="11.0\t81.*" />
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74 </assert_contents>
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75 </output>
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76 </test>
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77 </tests>
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78 <help><![CDATA[
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79 .. class:: infomark
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80
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81 **What it does**
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82
4
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83 This tool calculates and plots the angle between three atoms.
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84
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85 _____
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86
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87
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88 .. class:: infomark
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89
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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90 **Input**
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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91
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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92 - Trajectory file (DCD).
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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93 - PDB file.
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e7d0075052c9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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94 - Segment IDs, residue IDs and names of the three atoms for calculating angles.
e7d0075052c9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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95
e7d0075052c9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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96 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
e7d0075052c9 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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97
0
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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98 _____
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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99
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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100
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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101 .. class:: infomark
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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102
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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103 **Output**
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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104
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105 - Tab-separated file of raw data of the angle between three atoms calculated for each frame.
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fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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106 - Image (as png) of the time series graph.
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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107
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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108 ]]></help>
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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109 <expand macro="citations" />
fc7293c6cb6a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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110 </tool>