Mercurial > repos > jay > pdaug_peptide_cd_spectral_analysis
annotate PDAUG_Peptide_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.xml @ 1:9bbad349f44c draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
author | jay |
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date | Tue, 29 Dec 2020 04:45:46 +0000 |
parents | 6cff147419ab |
children | 370b68568ba2 |
rev | line source |
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0
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 <tool id="pdaug_peptide_cd_spectral_analysis" name="PDAUG Peptide CD Spectral Analysis" version="0.1.0" python_template_version="3.5"> |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 |
6cff147419ab
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3 <description>Circular dichroism data analysis</description> |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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4 |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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5 <requirements> |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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6 <requirement version="0.24.2" type="package" >pandas </requirement> |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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7 <requirement version="4.2.1" type="package" >modlamp </requirement> |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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8 </requirements> |
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9 <command detect_errors="exit_code"><![CDATA[ |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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10 |
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11 mkdir temp |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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12 |
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13 #for $i, $inp in enumerate($input1): |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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14 && ln -s '$inp' 'temp/${i}.csv' |
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15 #end for |
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16 |
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17 |
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18 && |
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19 |
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20 python $__tool_directory__/PDAUG_Peptide_CD_Spectral_Analysis.py '$SelMethods.Methods' |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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21 |
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22 #if $SelMethods.Methods == 'calc_ellipticity' |
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9bbad349f44c
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23 -T '$SelMethods.ellipticity' |
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24 -H 'temp' |
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25 -Wn '$SelMethods.Wn' |
9bbad349f44c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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26 -Wx '$SelMethods.Wx' |
9bbad349f44c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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27 -A '$SelMethods.Amide' |
9bbad349f44c
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28 -P '$SelMethods.Pathlen' |
9bbad349f44c
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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29 -O '$output2' |
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30 #end if |
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31 |
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32 #if $SelMethods.Methods == 'PlotData' |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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33 -T '$SelMethods.ellipticity' |
1
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34 -H 'temp' |
9bbad349f44c
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35 -Wn '$SelMethods.Wn' |
9bbad349f44c
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36 -Wx '$SelMethods.Wx' |
9bbad349f44c
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37 -A '$SelMethods.Amide' |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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38 -P '$SelMethods.Pathlen' |
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39 #end if |
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40 |
6cff147419ab
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41 #if $SelMethods.Methods == 'Dichroweb' |
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42 -T '$SelMethods.ellipticity' |
1
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43 -H 'temp' |
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44 -Wn '$SelMethods.Wn' |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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45 -Wx '$SelMethods.Wx' |
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46 -A '$SelMethods.Amide' |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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47 -P '$SelMethods.Pathlen' |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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48 #end if |
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49 |
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50 #if $SelMethods.Methods == 'helicity' |
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51 -H 'temp' |
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52 -Wn '$SelMethods.Wn' |
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53 -Wx '$SelMethods.Wx' |
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54 -A '$SelMethods.Amide' |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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55 -P '$SelMethods.Pathlen' |
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56 -t '$SelMethods.T' |
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57 -k '$SelMethods.K' |
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58 -I '$SelMethods.Induction' |
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59 -O $output1 |
6cff147419ab
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60 #end if |
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61 |
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62 ]]></command> |
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63 |
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64 |
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65 <inputs> |
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66 |
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67 <param name="input1" label="Input file" type="data" format="csv" multiple="true" argument= "--TrainFile"/> |
6cff147419ab
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68 |
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69 <conditional name='SelMethods' > |
6cff147419ab
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70 |
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71 <param name="Methods" type="select" label="Circular dichroism data analysis options" help="Circular dichroism data analysis options" > |
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72 <option value="calc_ellipticity">Calculate Ellipticity</option> |
6cff147419ab
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73 <option value="PlotData">Plot Data</option> |
6cff147419ab
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74 <option value="Dichroweb">Save data in DichroWeb readable format</option> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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75 <option value="helicity">Calculate the percentage of helicity</option> |
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76 </param> |
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77 |
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78 <when value="calc_ellipticity"> |
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79 <param name="ellipticity" type="select" label="Ellipticity type" argument="-T" help="Methods to calculate the molar ellipticity for all loaded data"> |
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80 <option value="calc_molar_ellipticity">Calculate Molar Ellipticity</option> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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81 <option value="calc_meanres_ellipticity">Calculate Mean Residue Ellipticity</option> |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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82 </param> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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83 <param name="Wn" type="integer" value="180" label="Smallest wavelength" argument="-Wn" help="Smallest wavelength measured" /> |
6cff147419ab
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84 <param name="Wx" type="integer" value="260" label="Highest wavelength" argument="-Wx" help="Highest wavelength measured" /> |
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85 <param name="Amide" type="boolean" label="Amide" value="true" argument="-A" help="Specifies whether the sequences have amidated C-termini" /> |
6cff147419ab
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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86 <param name="Pathlen" type="float" label="Pathlen" value="1.0" argument="--P" help="Cuvette path length in mm"/> |
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87 </when> |
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88 |
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89 <when value="PlotData"> |
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90 <param name="ellipticity" type="select" label="Which data should be plotted " argument=""> |
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91 <option value="mean residue ellipticity">Mean Residue Ellipticity</option> |
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92 <option value="molar ellipticity">Molar Ellipticity</option> |
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93 <option value="circular dichroism">Circular Dichroism</option> |
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94 </param> |
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95 <param name="Wn" type="integer" value="180" label="Smallest wavelength" argument="-Wn" help="Smallest wavelength measured" /> |
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96 <param name="Wx" type="integer" value="260" label="Highest wavelength" argument="-Wx" help="Highest wavelength measured" /> |
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97 <param name="Amide" type="boolean" label="Amide" value="true" argument="-A" help="Specifies whether the sequences have amidated C-termini" /> |
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98 <param name="Pathlen" type="float" label="Pathlen" value="1.0" argument="--P" help="Cuvette path length in mm"/> |
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99 </when> |
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100 |
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101 <when value="Dichroweb"> |
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102 <param name="ellipticity" type="select" label="which data should be return" argument=""> |
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103 <option value="mean residue ellipticity">Mean Residue Ellipticity</option> |
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104 <option value="molar ellipticity">Molar Ellipticity</option> |
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105 <option value="circular dichroism">Circular Dichroism</option> |
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106 </param> |
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107 <param name="Wn" type="integer" value="260" label="Smallest wavelength" argument="-Wn" help="Smallest wavelength measured" /> |
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108 <param name="Wx" type="integer" value="260" label="Highest wavelength" argument="-Wx" help="Highest wavelength measured" /> |
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109 <param name="Amide" type="boolean" label="Amide" value="true" argument="-A" help="Specifies whether the sequences have amidated C-termini" /> |
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110 <param name="Pathlen" type="float" label="Pathlen" value="1.0" argument="--P" help="Cuvette path length in mm"/> |
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111 </when> |
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112 |
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113 <when value="helicity"> |
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114 <param name="Wn" type="integer" value="260" label="Smallest wavelength" argument="-Wn" help="Smallest wavelength measured" /> |
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115 <param name="Wx" type="integer" value="260" label="Highest wavelength" argument="-Wx" help="Highest wavelength measured" /> |
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116 <param name="Amide" type="boolean" label="Amide" value="true" argument="-A" help="Specifies whether the sequences have amidated C-termini" /> |
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117 <param name="Pathlen" type="float" label="Pathlen" value="1.0" argument="--P" help="Cuvette path length in mm"/> |
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118 <param name="T" type="float" label="Temperature" value="24.0" help="Experiment temperature in C" argument="-T"/> |
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119 <param name="K" type="float" label="Finite length correction factor" value ="2.4" help="Finite length correction factor" argument="-k" /> |
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120 <param name="Induction" type="boolean" label="Induction" value="true" help="Wether the helical induction upon changing from one solvent to another should be calculated" /> |
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121 </when> |
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122 |
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123 </conditional> |
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124 </inputs> |
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125 |
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126 <outputs> |
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127 |
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128 <data name="output1" format="tsv" label="${tool.name} on $on_string - ${SelMethods.Methods} (tabular)" > |
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129 <filter> SelMethods['Methods'] == 'helicity' </filter> |
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130 </data> |
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131 |
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132 <data name="output2" format="tsv" label="${tool.name} on $on_string - ${SelMethods.Methods} (tabular)" > |
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133 <filter> SelMethods['Methods'] == 'calc_ellipticity' </filter> |
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134 </data> |
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135 |
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136 <collection name="pdfout" type="list" label="${tool.name} on $on_string - ${SelMethods.Methods} (PDFs)"> |
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137 <discover_datasets pattern="__name_and_ext__" format='pdf' directory="temp/PDF" /> |
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138 <filter> SelMethods['Methods'] == 'PlotData' </filter> |
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139 </collection> |
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140 |
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141 |
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142 <collection name="dichroout" type="list" label="${tool.name} on $on_string - ${SelMethods.Methods} (Dichro)"> |
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143 <discover_datasets pattern="__name_and_ext__" format='tsv' directory="temp/Dichro" /> |
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144 <filter> SelMethods['Methods'] == 'Dichroweb' </filter> |
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145 </collection> |
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146 |
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147 </outputs> |
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148 |
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149 <tests> |
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150 |
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151 <test> |
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152 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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153 <param name="Methods" value="calc_ellipticity"/> |
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154 <param name="ellipticity" value="calc_molar_ellipticity" /> |
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155 <param name="Wn" value="180" /> |
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156 <param name="Wx" value="260" /> |
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157 <param name="Amide" value="true" /> |
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158 <param name="Pathlen" value="1.0" /> |
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159 <output name="output1" file="calc_molar_ellipticity.tsv" /> |
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160 </test> |
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161 |
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162 <test> |
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163 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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164 <param name="Methods" value="calc_ellipticity"/> |
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165 <param name="ellipticity" value="calc_meanres_ellipticity" /> |
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166 <param name="Wn" value="180" /> |
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167 <param name="Wx" value="260" /> |
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168 <param name="Amide" value="true" /> |
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169 <param name="Pathlen" value="1.0" /> |
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170 <output name="output1" file="calc_meanres_ellipticity.tsv" /> |
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171 </test> |
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172 |
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173 <test> |
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174 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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175 <param name="Methods" value="PlotData"/> |
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176 <param name="ellipticity" value="mean residue ellipticity" /> |
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177 <param name="Wn" value="180" /> |
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178 <param name="Wx" value="260" /> |
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179 <param name="Amide" value="false" /> |
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180 <param name="Pathlen" value="1.0" /> |
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181 |
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182 <output_collection name="pdfout" count="3" > |
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183 </output_collection> |
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184 |
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185 </test> |
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186 |
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187 <test> |
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188 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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189 <param name="Methods" value="calc_ellipticity"/> |
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190 <param name="ellipticity" value="calc_molar_ellipticity" /> |
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191 <param name="Wn" value="180" /> |
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192 <param name="Wx" value="260" /> |
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193 <param name="Amide" value="true" /> |
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194 <param name="Pathlen" value="1.0" /> |
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195 <output name="output1" file="calc_molar_ellipticity.tsv" /> |
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196 </test> |
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197 |
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198 <test> |
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199 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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200 <param name="Methods" value="calc_ellipticity"/> |
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201 <param name="ellipticity" value="calc_meanres_ellipticity" /> |
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202 <param name="Wn" value="180" /> |
6cff147419ab
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203 <param name="Wx" value="260" /> |
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204 <param name="Amide" value="true" /> |
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205 <param name="Pathlen" value="1.0" /> |
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206 <output name="output1" file="calc_meanres_ellipticity.tsv" /> |
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207 </test> |
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208 |
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209 |
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210 |
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211 <test> |
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212 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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213 <param name="Methods" value="PlotData"/> |
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214 <param name="ellipticity" value="mean residue ellipticity" /> |
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215 <param name="Wn" value="180" /> |
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216 <param name="Wx" value="260" /> |
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217 <param name="Amide" value="false" /> |
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218 <param name="Pathlen" value="1.0" /> |
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219 <output_collection name="pdfout" type="pdf" > |
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220 </output_collection> |
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221 </test> |
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222 |
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223 <test> |
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224 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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225 <param name="Methods" value="PlotData"/> |
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226 <param name="ellipticity" value="molar ellipticity" /> |
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227 <param name="Wn" value="180" /> |
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228 <param name="Wx" value="260" /> |
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229 <param name="Amide" value="false" /> |
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230 <param name="Pathlen" value="1.0" /> |
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231 <output_collection name="pdfout" type="pdf" > |
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232 </output_collection> |
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233 </test> |
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234 |
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235 <test> |
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236 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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237 <param name="Methods" value="PlotData"/> |
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238 <param name="ellipticity" value="circular dichroism" /> |
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239 <param name="Wn" value="180" /> |
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240 <param name="Wx" value="260" /> |
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241 <param name="Amide" value="false" /> |
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242 <param name="Pathlen" value="1.0" /> |
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243 <output_collection name="pdfout" type="pdf" > |
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244 </output_collection> |
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245 </test> |
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246 <test> |
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247 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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248 <param name="Methods" value="Dichroweb"/> |
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249 <param name="ellipticity" value="mean residue ellipticity" /> |
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250 <param name="Wn" value="180" /> |
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251 <param name="Wx" value="260" /> |
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252 <param name="Amide" value="false" /> |
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253 <param name="Pathlen" value="1.0" /> |
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254 <output_collection name="dichroout" type="tabular"> |
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255 </output_collection> |
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256 </test> |
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257 |
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258 <test> |
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259 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
6cff147419ab
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260 <param name="Methods" value="Dichroweb"/> |
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261 <param name="ellipticity" value="molar ellipticity" /> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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262 <param name="Wn" value="180" /> |
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263 <param name="Wx" value="260" /> |
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264 <param name="Amide" value="false" /> |
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265 <param name="Pathlen" value="1.0" /> |
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266 <output_collection name="dichroout" type="tabular" > |
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267 </output_collection> |
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268 </test> |
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269 |
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270 <test> |
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271 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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272 <param name="Methods" value="Dichroweb"/> |
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273 <param name="ellipticity" value="circular dichroism" /> |
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274 <param name="Wn" value="180" /> |
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275 <param name="Wx" value="260" /> |
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276 <param name="Amide" value="false" /> |
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277 <param name="Pathlen" value="1.0" /> |
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278 <output_collection name="dichroout" type="tabular"> |
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279 </output_collection> |
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280 </test> |
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281 |
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282 <test> |
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283 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" /> |
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284 <param name="Methods" value="helicity"/> |
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285 <param name="Wn" value="180" /> |
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286 <param name="Wx" value="260" /> |
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287 <param name="Amide" value="false" /> |
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288 <param name="Pathlen" value="1.0" /> |
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289 <param name="T" value="24" /> |
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290 <param name="K" value="3.5" /> |
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291 <param name="Induction" value="false" /> |
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292 <output name="output1" value="helicity.tsv" /> |
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293 |
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294 </test> |
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295 |
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296 </tests> |
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297 |
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298 <help><![CDATA[ |
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299 .. class:: infomark |
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300 |
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301 **What it does** |
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302 |
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303 This tool handles circular dichroism data files and calculates several ellipticity and helicity values. The class can handle data files of the Applied Photophysics type. For explanations of different units used in CD spectroscopy, visit https://www.photophysics.com/resources/7-cd-units-conversions. Provided with four different options. |
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304 |
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305 * **Calculate Ellipticity** Calculates molar and mean residue ellipticity. |
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306 * **Plot Data** Generates circular_dichroism plots for all read data in the initial directory. |
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307 * **Save data in DichroWeb readable format** Method to save the calculated CD data into DichroWeb readable format (semi-colon separated). The produced files can then directly be uploaded to the DichroWeb analysis tool. |
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308 * **Calculate the percentage of helicity** Method to calculate the percentage of helicity out of the mean residue ellipticity data. The calculation is based on the formula by Fairlie and co-workers. |
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309 |
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310 ----- |
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311 |
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312 **Inputs** |
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313 |
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314 **1** calc_ellipticity |
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315 * **--Type** |
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316 * **--Wmin** smallest wavelength measured |
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317 * **--Wmax** highest wavelength measured |
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318 * **--Amide** specifies whether the sequences have amidated C-termini |
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319 * **--Pathlen** cuvette path length in mm |
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320 |
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321 **2** PlotData |
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322 * **--Type** |
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323 * **--Wmin** smallest wavelength measured |
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324 * **--Wmax** highest wavelength measured |
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325 * **--Amide** specifies whether the sequences have amidated C-termini |
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326 * **--Pathlen** cuvette path length in mm |
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327 |
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328 **3** Dicroweb |
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329 * **--Type** |
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330 * **--Wmin** smallest wavelength measured |
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331 * **--Wmax** highest wavelength measured |
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332 * **--Amide** specifies whether the sequences have amidated C-termini |
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333 * **--Pathlen** cuvette path length in mm |
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334 |
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335 **4** helicity |
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336 * **--Type** |
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337 * **--Wmin** smallest wavelength measured |
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338 * **--Wmax** highest wavelength measured |
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339 * **--Amide** specifies whether the sequences have amidated C-termini |
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340 * **--Pathlen** cuvette path length in mm |
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341 * **--temperature** experiment temperature in °C |
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342 * **--k** {float, 2.4 - 4.5} finite length correction factor. Can be adapted to the helicity of a known peptide. |
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343 * **--Induction** whether the helical induction upon changing from one solvent to another should be calculated. |
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344 |
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345 |
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346 ----- |
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347 |
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348 **Outputs** |
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349 * **Calculate Ellipticity** Return molar or mean residue ellipticity as a tabular file. |
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350 * **Plot Data** Returns PDF files. |
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351 * **Save data in DichroWeb readable format** Returns tabular files. |
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352 * **Calculate the percentage of helicity** Returns approximate helicity for every sequence as a tabular file.]]></help> |
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353 <citations> |
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354 <citation type="bibtex"> |
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355 @misc{PDAUGGITHUB, |
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356 author = {Joshi, Jayadev and Blankenberg, Daniel}, |
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357 year = {2020}, |
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358 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, |
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359 publisher = {GitHub}, |
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360 journal = {GitHub repository}, |
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361 url = |
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362 {https://github.com/jaidevjoshi83/pdaug.git}, |
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363 } |
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364 </citation> |
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365 |
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366 <citation type="bibtex"> |
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367 @article{müller_gabernet_hiss_schneider_2017, |
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368 title={modlAMP: Python for antimicrobial peptides}, |
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369 volume={33}, |
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370 DOI={10.1093/bioinformatics/btx285}, |
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371 number={17}, |
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372 journal={Bioinformatics}, |
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373 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, |
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374 year={2017}, |
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375 pages={2753–2755} |
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376 } |
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377 </citation> |
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378 </citations> |
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379 </tool> |