Mercurial > repos > chemteam > mdanalysis_dihedral

annotate dihedrals.xml @ 6:0493024c3318 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 7a25958195ccc8f448dd64ddcc36e8f5e5979d8b"
author chemteam
date Wed, 20 May 2020 13:06:08 -0400
parents d8178fe9aaff
children aaa130695a2b
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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@">
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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>
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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 '$__tool_directory__/dihedrals.py'
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10 --itraj '$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 --isegid4 '$segid4'
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24 --iresid4 '$resid4'
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25 --iname4 '$name4'
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26 --output '$output'
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27 --odihedral_plot '$dihedral_plot'
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28 2>&1
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29 ]]></command>
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30 <inputs>
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31 <expand macro="analysis_inputs"/>
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32 <param name="segid1" type="text" value="PRO" label="Segment ID of atom 1"/>
d8178fe9aaff "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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33 <param name="resid1" type="text" value="212" label="Residue ID of atom 1"/>
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34 <param name="name1" type="text" value="OE2" label="Atom name of atom 1"/>
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35 <param name="segid2" type="text" value="HET" label="Segment ID of atom 2"/>
d8178fe9aaff "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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36 <param name="resid2" type="text" value="3" label="Residue ID of atom 2"/>
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37 <param name="name2" type="text" value="C1" label="Atom name of atom 2"/>
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38 <param name="segid3" type="text" value="HET" label="Segment ID of atom 3"/>
d8178fe9aaff "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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39 <param name="resid3" type="text" value="3" label="Residue ID of atom 3"/>
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40 <param name="name3" type="text" value="C2" label="Atom name of atom 3"/>
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41 <param name="segid4" type="text" value="HET" label="Segment ID of atom 4"/>
d8178fe9aaff "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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42 <param name="resid4" type="text" value="3" label="Residue ID of atom 4"/>
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43 <param name="name4" type="text" value="C3" label="Atom name of atom 4"/>
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44 </inputs>
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45 <outputs>
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46 <data format="tabular" name="output" label="Dihedral analysis raw data"/>
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47 <data format="png" name="dihedral_plot" label="Dihedral analysis plot"/>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <expand macro="tests_inputs"/>
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52 <param name="segid1" value="PRO"/>
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53 <param name="resid1" value="212"/>
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54 <param name="name1" value="OE2"/>
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55 <param name="segid2" value="HET"/>
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56 <param name="resid2" value="3"/>
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57 <param name="name2" value="C1"/>
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58 <param name="segid3" value="HET"/>
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59 <param name="resid3" value="3"/>
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60 <param name="name3" value="C2"/>
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61 <param name="segid4" value="HET"/>
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62 <param name="resid4" value="3"/>
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63 <param name="name4" value="C3"/>
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64 <output name="output" file="Dihedral_analysis_raw_data.tabular" />
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65 </test>
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66 <test>
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67 <expand macro="tests_inputs_gmx"/>
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68 <param name="segid1" value="SYSTEM"/>
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69 <param name="resid1" value="212"/>
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70 <param name="name1" value="OE2"/>
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71 <param name="segid2" value="SYSTEM"/>
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72 <param name="resid2" value="3"/>
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73 <param name="name2" value="C1"/>
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74 <param name="segid3" value="SYSTEM"/>
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75 <param name="resid3" value="3"/>
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76 <param name="name3" value="C2"/>
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77 <param name="segid4" value="SYSTEM"/>
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78 <param name="resid4" value="3"/>
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79 <param name="name4" value="C3"/>
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80 <output name="output">
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81 <assert_contents>
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82 <has_n_columns n="2" />
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83 <has_line_matching expression="0\t-61.*" />
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84 <has_line_matching expression="12\t-76.*" />
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85 <has_line_matching expression="4\t-66.*" />
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86 </assert_contents>
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87 </output>
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88 </test>
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89 </tests>
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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90 <help><![CDATA[
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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91 .. class:: infomark
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92
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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93 **What it does**
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94
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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95 This tool calculates and plots dihedral angles (angle between two intersecting planes) between four atoms.
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96
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97 _____
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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98
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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99
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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100 .. class:: infomark
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101
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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102 **Input**
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103
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104 - Trajectory file (DCD).
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105 - PDB file.
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106 - Segment IDs, residue IDs and names of the four atoms to calculate the dihedral angle.
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107
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108 Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.
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109
0
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110 _____
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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111
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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112
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113 .. class:: infomark
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114
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115 **Output**
f95d4348ed7c planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit c32fe331f438df7760084b27bafad9f78f01edde
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116
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117 - Tab-separated file of raw data of the dihedral angle calculated for each frame.
0
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118 - Image (as png) of the time series graph.
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119
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120 ]]></help>
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121 <expand macro="citations" />
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122 </tool>