Mercurial > repos > jay > pdaug_peptide_cd_spectral_analysis

annotate PDAUG_Peptide_CD_Spectral_Analysis/PDAUG_Peptide_CD_Spectral_Analysis.xml @ 6:370b68568ba2 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author jay
date Sun, 31 Jan 2021 02:46:28 +0000
parents 9bbad349f44c
children
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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">
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3 <description>Circular dichroism data analysis</description>
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5 <requirements>
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6 <requirement version="0.24.2" type="package" >pandas </requirement>
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7 <requirement version="4.2.1" type="package" >modlamp </requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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11 mkdir temp
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13 #for $i, $inp in enumerate($input1):
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14 && ln -s '$inp' 'temp/${i}.csv'
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15 #end for
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18 &&
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20 python $__tool_directory__/PDAUG_Peptide_CD_Spectral_Analysis.py '$SelMethods.Methods'
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22 #if $SelMethods.Methods == 'calc_ellipticity'
1
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23 -T '$SelMethods.ellipticity'
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24 -H 'temp'
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25 -Wn '$SelMethods.Wn'
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26 -Wx '$SelMethods.Wx'
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27 -A '$SelMethods.Amide'
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28 -P '$SelMethods.Pathlen'
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29 -O '$output2'
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30 #end if
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32 #if $SelMethods.Methods == 'PlotData'
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33 -T '$SelMethods.ellipticity'
1
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34 -H 'temp'
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35 -Wn '$SelMethods.Wn'
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36 -Wx '$SelMethods.Wx'
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37 -A '$SelMethods.Amide'
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38 -P '$SelMethods.Pathlen'
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39 #end if
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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 '$SelMethods.Wn'
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45 -Wx '$SelMethods.Wx'
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46 -A '$SelMethods.Amide'
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47 -P '$SelMethods.Pathlen'
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48 #end if
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49
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50 #if $SelMethods.Methods == 'helicity'
1
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51 -H 'temp'
0
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52 -Wn '$SelMethods.Wn'
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53 -Wx '$SelMethods.Wx'
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54 -A '$SelMethods.Amide'
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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
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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"/>
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69 <conditional name='SelMethods' >
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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>
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73 <option value="PlotData">Generate CD Plots</option>
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74 <option value="Dichroweb">Save Data in DichroWeb Readable Format</option>
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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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81 <option value="calc_meanres_ellipticity">Calculate Mean Residue Ellipticity</option>
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82 </param>
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83 <param name="Wn" type="integer" value="180" label="Smallest wavelength" argument="-Wn" help="Smallest wavelength measured" />
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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" />
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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 - ${SelMethods.Methods} (tabular)" >
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129 <filter> SelMethods['Methods'] == 'helicity' </filter>
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130 </data>
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131
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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132 <data name="output2" format="tsv" label="${tool.name} on $on_string - ${SelMethods.Methods} (tabular)" >
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133 <filter> SelMethods['Methods'] == 'calc_ellipticity' </filter>
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134 </data>
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135
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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136 <collection name="pdfout" type="list" label="${tool.name} on $on_string - ${SelMethods.Methods} (PDFs)">
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137 <discover_datasets pattern="__name_and_ext__" format='pdf' directory="temp/PDF" />
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138 <filter> SelMethods['Methods'] == 'PlotData' </filter>
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139 </collection>
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140
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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141
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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142 <collection name="dichroout" type="list" label="${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
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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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
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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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
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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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
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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182 <output_collection name="pdfout" count="3" >
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183 </output_collection>
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184
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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185 </test>
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186
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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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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diff changeset
190 <param name="ellipticity" value="calc_molar_ellipticity" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
191 <param name="Wn" value="180" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
192 <param name="Wx" value="260" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
193 <param name="Amide" value="true" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
194 <param name="Pathlen" value="1.0" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
195 <output name="output1" file="calc_molar_ellipticity.tsv" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
196 </test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
197
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
198 <test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
199 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
200 <param name="Methods" value="calc_ellipticity"/>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
201 <param name="ellipticity" value="calc_meanres_ellipticity" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
202 <param name="Wn" value="180" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
203 <param name="Wx" value="260" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
204 <param name="Amide" value="true" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
205 <param name="Pathlen" value="1.0" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
206 <output name="output1" file="calc_meanres_ellipticity.tsv" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
207 </test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
208
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
209
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
210
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
211 <test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
212 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
213 <param name="Methods" value="PlotData"/>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
214 <param name="ellipticity" value="mean residue ellipticity" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
215 <param name="Wn" value="180" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
216 <param name="Wx" value="260" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
217 <param name="Amide" value="false" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
218 <param name="Pathlen" value="1.0" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
219 <output_collection name="pdfout" type="pdf" >
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
220 </output_collection>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
221 </test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
222
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
223 <test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
224 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
225 <param name="Methods" value="PlotData"/>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
226 <param name="ellipticity" value="molar ellipticity" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
227 <param name="Wn" value="180" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
228 <param name="Wx" value="260" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
229 <param name="Amide" value="false" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
230 <param name="Pathlen" value="1.0" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
231 <output_collection name="pdfout" type="pdf" >
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
232 </output_collection>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
233 </test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
234
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
235 <test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
236 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
237 <param name="Methods" value="PlotData"/>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
238 <param name="ellipticity" value="circular dichroism" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
239 <param name="Wn" value="180" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
240 <param name="Wx" value="260" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
241 <param name="Amide" value="false" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
242 <param name="Pathlen" value="1.0" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
243 <output_collection name="pdfout" type="pdf" >
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
244 </output_collection>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
245 </test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
246 <test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
247 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
248 <param name="Methods" value="Dichroweb"/>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
249 <param name="ellipticity" value="mean residue ellipticity" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
250 <param name="Wn" value="180" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
251 <param name="Wx" value="260" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
252 <param name="Amide" value="false" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
253 <param name="Pathlen" value="1.0" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
254 <output_collection name="dichroout" type="tabular">
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
255 </output_collection>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
256 </test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
257
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
258 <test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
259 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
260 <param name="Methods" value="Dichroweb"/>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
261 <param name="ellipticity" value="molar ellipticity" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
262 <param name="Wn" value="180" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
263 <param name="Wx" value="260" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
264 <param name="Amide" value="false" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
265 <param name="Pathlen" value="1.0" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
266 <output_collection name="dichroout" type="tabular" >
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
267 </output_collection>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
268 </test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
269
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
270 <test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
271 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
272 <param name="Methods" value="Dichroweb"/>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
273 <param name="ellipticity" value="circular dichroism" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
274 <param name="Wn" value="180" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
275 <param name="Wx" value="260" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
276 <param name="Amide" value="false" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
277 <param name="Pathlen" value="1.0" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
278 <output_collection name="dichroout" type="tabular">
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
279 </output_collection>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
280 </test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
281
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
282 <test>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
283 <param name="input1" value="Peptide1_T.csv,Peptide2_W.csv" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
284 <param name="Methods" value="helicity"/>
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
285 <param name="Wn" value="180" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
286 <param name="Wx" value="260" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
287 <param name="Amide" value="false" />
6cff147419ab "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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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 * **Generate CD Plots** 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.
0
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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** Calculate 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** Generate CD Plots
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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** Save Data in DichroWeb Readable Format
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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** Calculate the Percentage of 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 **Outputs**
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348 * **Calculate Ellipticity** Return molar or mean residue ellipticity as a tabular file.
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349 * **Plot Data** Returns PDF files.
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350 * **Save data in DichroWeb readable format** Returns tabular files.
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351 * **Calculate the percentage of helicity** Returns approximate helicity for every sequence as a tabular file.]]></help>
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352 <citations>
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353 <citation type="bibtex">
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354 @misc{PDAUGGITHUB,
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355 author = {Joshi, Jayadev and Blankenberg, Daniel},
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356 year = {2020},
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357 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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358 publisher = {GitHub},
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359 journal = {GitHub repository},
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360 url =
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361 {https://github.com/jaidevjoshi83/pdaug.git},
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362 }
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363 </citation>
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364
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365 <citation type="bibtex">
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366 @article{müller_gabernet_hiss_schneider_2017,
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367 title={modlAMP: Python for antimicrobial peptides},
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368 volume={33},
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369 DOI={10.1093/bioinformatics/btx285},
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370 number={17},
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371 journal={Bioinformatics},
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372 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert},
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373 year={2017},
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374 pages={2753–2755}
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375 }
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376 </citation>
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377 </citations>
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378 </tool>