Mercurial > repos > chemteam > mdanalysis_ramachandran_protein

annotate ramachandran_auto_protein.xml @ 0:0f270722aca6 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
author chemteam
date Mon, 24 Aug 2020 16:27:56 -0400
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1 <tool id="mdanalysis_ramachandran_protein" name="Ramachandran Analysis" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>- Ramachandran plot for proteins</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="0.10.0">seaborn</requirement>
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9 <requirement type="package" version="2.10.0">h5py</requirement>
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10 <requirement type="package" version="2.11.1">jinja2</requirement>
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11 </expand>
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12 <command detect_errors="exit_code"><![CDATA[
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13 python '$__tool_directory__/ramachandran_auto_protein.py'
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14 --itraj '$trajin'
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15 --istr '$strin'
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16 --itrajext '$trajin.ext'
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17 --istrext '$strin.ext'
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18 --isegid1 '$segid1'
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19 #if $resid1 and $resid2:
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20 --iresid1 '$resid1'
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21 --iresid2 '$resid2'
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22 #end if
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23 #if $resname:
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24 --iresname '$resname'
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25 #end if
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26 --itemplatepath '$__tool_directory__'
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27 #if $groupby:
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28 --igroupby '$groupby'
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29 #end if
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30 --o_plot1 '$o_plot1'
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31 --o_plot2 '$o_plot2'
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32 --o_data1 '$o_data1'
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33 --o_html1 '$o_html1'
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34 2>&1
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35 ]]></command>
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36 <inputs>
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37 <expand macro="analysis_inputs" />
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38 <param name="segid1" type="text" value="PROA" label="Segment ID of the protein" help="A valid segment ID selection for the current molecular system">
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39 <validator type="regex" message="Maximum of 8 characters allowed.">^[a-zA-Z0-9]{1,8}$</validator>
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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40 </param>
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41 <param name="groupby" type="select" optional="true" label="Groupby analysis" help="Optional, create a groupby of the selection using residue name or id">
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42 <option value="name">ResidueName</option>
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43 <option value="id">ResidueID</option>
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44 </param>
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45 <param name="resname" optional="true" type="text" label="Residue Name" help="Optional, choose a residue name to refine the selection, e.g. ALA">
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46 <validator type="regex" message="Maximum of 8 characters allowed.">^[a-zA-Z0-9]{1,8}$</validator>
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47 </param>
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48 <param name="resid1" optional="true" type="text" label="start Residue ID" help="Optional, choose a residue ID to refine the selection, e.g. 5">
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49 <validator type="regex" message="Maximum of 6 digits allowed.">^[0-9]{1,6}$</validator>
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50 </param>
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51 <param name="resid2" optional="true" type="text" label="end Residue ID" help="Optional, choose a residue ID to refine the selection, e.g. 10">
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52 <validator type="regex" message="Maximum of 6 digits allowed.">^[0-9]{1,6}$</validator>
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53 </param>
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54 </inputs>
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55 <outputs>
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56 <data format="png" name="o_plot1" label="MDAnalysis Ramachandran plot" />
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57 <data format="png" name="o_plot2" label="Seaborn Ramachandran plot" />
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58 <data format="h5" name="o_data1" label="Ramachandran in HDF5 format" />
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59 <data format="html" name="o_html1" label="Ramachandran plot summary" />
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="trajin" value="test.dcd" ftype="dcd" />
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64 <param name="strin" value="test.pdb" ftype="pdb" />
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65 <param name="segid1" value="PRO" />
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66 <param name="groupby" value="name" />
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67 <output name="o_html1">
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68 <assert_contents>
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69 <has_text text="table" />
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70 <has_text text="(segid PRO) and resname MET" />
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71 <has_text text="(segid PRO) and resname VAL" />
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72 </assert_contents>
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73 </output>
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74 <output name="o_plot1">
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75 <assert_contents>
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76 <has_size value="53682" delta="3000" />
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77 </assert_contents>
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78 </output>
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79 <output name="o_plot2">
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80 <assert_contents>
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81 <has_size value="31740" delta="3000" />
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82 </assert_contents>
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83 </output>
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84 <output name="o_data1">
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85 <assert_contents>
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86 <has_size value="293824" delta="3000" />
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87 </assert_contents>
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88 </output>
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89 </test>
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90 </tests>
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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91 <help><![CDATA[
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92 .. class:: infomark
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93
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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94 **What it does**
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95
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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96 Creates a Ramachandran plot for proteins. All protein [φ,ψ] angles for a given segment ID are automatically selected for an entire trajectory and an averaged Ramachandran plot is returned. Optionally the selection can be refined by residue ID or residue name. Optionally the average Ramachandran plot can be deconvoluted and returned grouped by residue name or residue ID.
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97
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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98
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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99 _____
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100
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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101
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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102 .. class:: infomark
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103
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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104 **Input**
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105
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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106 - Structure file (PDB)
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107 - Trajectory file (DCD).
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108 - Segment ID
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109 - Optionally: Group data by residue name or residue ID
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110 - Optionally: refine selection by residue ID range or residue name (e.g. ALA)
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111
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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112 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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113
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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114 _____
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115
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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116
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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117 .. class:: infomark
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118
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119 **Output**
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120
0f270722aca6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 1b23e024af45cc0999d9142d07de6897d4189ec2"
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121 - Image (as png) of the Ramachandran from MDanalyis with the allowed regions as a background.
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122 - Image (as png) of the Ramachandran plot as a distribution.
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123 - Data (H5 format). All phi, psi timeseries raw data in HDF5 format.
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124 - All plot images tabulated (in html). To view the HTML in Galaxy this tool must be added to the allowlist by a Galaxy Admin.
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125 ]]></help>
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126 <expand macro="citations" />
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127 </tool>