annotate ramachandran_plots.xml @ 6:be5eaea0b2d1 draft default tip

"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit f1c3c88c7395f2e84cbc533199406aadb79c5c07"
author chemteam
date Fri, 13 Nov 2020 19:44:38 +0000
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1 <tool id="mdanalysis_ramachandran_plot" name="Ramachandran Plots" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>- calculate and plot the distribution of two dihedrals in a trajectory</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="1.5.2">scipy</requirement>
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9 <requirement type="package" version="0.10.0">seaborn</requirement>
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10 <requirement type="package" version="2.0.0">nbdime</requirement>
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11 <requirement type="package" version="5.3.1">pyyaml</requirement>
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12 </expand>
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13 <command detect_errors="exit_code"><![CDATA[
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14 python '$__tool_directory__/ramachandran_plots.py'
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15 --itraj '$trajin'
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16 --istr '$strin'
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17 --itrajext '$trajin.ext'
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18 --istrext '$strin.ext'
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19 --iyml '$ymlin'
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20 --output '$output'
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21 --oramachandran_plot '$ramachandran_plot'
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22 2>&1
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23 ]]></command>
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24 <inputs>
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25 <expand macro="analysis_inputs" />
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26 <section name="ymlparam" title="Torsion Parameters" expanded="False">
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27 <param format="txt" name="ymlin" type="data" label="Torsion parameters in yml format" help="Information in YAML format about the segid, resid, and name for atoms 1-4 of the phi and psi angles. Example formatting included in the main help text"/>
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28 </section>
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29 </inputs>
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30 <outputs>
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31 <data format="tabular" name="output" label="Ramachandran Plot raw data" />
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32 <data format="png" name="ramachandran_plot" label="Ramachandran Plot" />
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="trajin" value="test.dcd" ftype="dcd" />
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37 <param name="strin" value="test.pdb" ftype="pdb" />
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38 <section name="ymlparam">
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39 <param name="ymlin" value="test.yml" />
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40 </section>
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41 <output name="output">
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42 <assert_contents>
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43 <has_text text="-144.503" />
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44 <has_text text="-140.553" />
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45 </assert_contents>
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46 </output>
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47 <output name="ramachandran_plot">
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48 <assert_contents>
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49 <has_size value="18522" delta="2000" />
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50 </assert_contents>
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51 </output>
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 .. class:: infomark
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56
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57 **What it does**
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58
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59 A Ramachandran plot ([φ,ψ] plot) was originally developed as a way to visualize the energetically allowed regions for backbone dihedral angles ψ and φ of an amino acid.
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60 It can be also used to calculate glycosidic φ and ψ angles formed between carbohydrates. This tool can calculate and plot the histogram (Ramachandran plot) of user-defined φ and ψ angles of a trajectory.
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61
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62
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63 _____
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64
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65
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66 .. class:: infomark
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67
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68 **Input**
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69
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70 - Trajectory file (DCD).
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71 - PDB file.
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72 - Text file in YAML format with Segment IDs, residue IDs and names of the four atoms to calculate dihedrals.
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73
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74 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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75
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76 - For protein φ and ψ dihedral definitions see https://proteinstructures.com/Structure/Structure/Ramachandran-plot.html
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77 - For glycan φ and ψ dihedral definitions, see
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78 - `Glycan Structure Website`_ - The glycosidic torsion angle definition is adopted from the crystallographic definition; O5-C1-O1-C'x (Φ; phi), C1-O1-C'x-C'x-1 (Ψ; psi), and O1-C'6-C'5-O'5 (ω; omega). The torsion angle between the first residue of the N-glycan chain and the side chain of the asparagine residue is defined as O5-C1-N'D2-C'G (Φ; phi) and C1-N'D2-C'G-C'B (Ψ; psi). The torsion angle between the first residue of the O-glycan chain and the side chain of the serine residue is defined as O5-C1-O'G-C'B (Φ; phi) and C1-O'G-C'B-C'A (Ψ; psi). For threonine residue, OG1 is used instead of OG. The atom names are based on the CHARMM topology.
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79 - `Glycosciences Website`_ - NMR definition - Φ phi: H1-C1-O1-C′X Ψ psi: C1-O1-C′X-H′X ω omega: O1-C′6-C′5-H′5 Crystallographic definition - Φ phi: O5-C1-O1-C′X Ψ psi: C1-O1-C′X-C′X+1 ω omega: O1-C′6-C′5-O′5
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80
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81 - An example of a yaml formatted selection for φ-ψ of a small glycoprotein called PROF with a carbohydrate portion called CARA where φ=O5-C1-OG1-CB1 and ψ=C1-OG1-CB-CA for the selected segment and residue ids.
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82
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83 .. code-block:: yaml
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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84
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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85 ramachandran1:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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86 phi:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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87 atom1:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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88 segid: CARA
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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89 resid: 1
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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90 name: O5
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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91 atom2:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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92 segid: CARA
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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93 resid: 1
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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94 name: C1
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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95 atom3:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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96 segid: PROF
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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97 resid: 4
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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98 name: OG1
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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99 atom4:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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100 segid: PROF
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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101 resid: 4
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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102 name: CB
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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103 psi:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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104 atom1:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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105 segid: CARA
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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106 resid: 1
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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107 name: C1
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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108 atom2:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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109 segid: PROF
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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110 resid: 4
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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111 name: OG1
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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112 atom3:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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113 segid: PROF
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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114 resid: 4
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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115 name: CB
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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116 atom4:
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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117 segid: PROF
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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118 resid: 4
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
chemteam
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119 name: CA
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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120 comment: pick visually using VMD using labels. Go to labels, dihedral to see the information about resname resid and atomname and then lookup the segname for ach atom.
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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121
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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122 _____
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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123
4
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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124
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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125 .. class:: infomark
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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126
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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127 **Output**
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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128
1
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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129 - Tab-separated file of raw data of the φ,ψ angles over time.
ce0728b92289 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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130 - Image (as png) of the Ramachandran plot.
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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131
4
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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132 .. _`Glycan Structure Website`: http://www.glycanstructure.org/fragment-db/howto
70a2d548e62c "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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133 .. _`Glycosciences Website`: http://www.glycosciences.de/tools/glytorsion/
0
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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134 ]]></help>
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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135 <expand macro="citations" />
d710c7f00ae6 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3ff06e3182c3a1546ea0a3b29e0d4383e12169e1
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136 </tool>