Mercurial > repos > jay > pdaug_sequence_property_based_descriptors

annotate PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.xml @ 0:6b6aec52638d draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 02:23:51 +0000
parents
children 7dc979925e31
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1 <tool id="pdaug_sequence_property_based_descriptors" name="PDAUG Sequence Property Based Descriptors" version="0.1.0">
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2 <description>Calculates sequence based descriptors of the peptide sequences</description>
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4 <requirements>
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5 <requirement type="package" version="2.7.18">python</requirement>
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6 <requirement type="package" version="0.24.2">pandas</requirement>
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7 <requirement type="package" version="1.0">pydpi</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1" level="fatal" />
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11 </stdio>
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12 <command detect_errors="exit_code"><![CDATA[
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14 python '$__tool_directory__/PDAUG_Sequence_Property_Based_Descriptors.py' --InFile '$input1'
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16 --DesType '$SelectDiscriptor.DesType'
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18 #if '$SelectDiscriptor.DesType' == 'PAAC'
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19 --Lamda '$SelectDiscriptor.Lamda'
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20 --Weight '$SelectDiscriptor.Weight'
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21 #end if
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23 #if $SelectDiscriptor.DesType == 'APAAC'
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24 --Lamda '$SelectDiscriptor.Lamda'
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25 --Weight '$SelectDiscriptor.Weight'
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26 #end if
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28 #if $SelectDiscriptor.DesType == 'All'
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29 --Lamda '$SelectDiscriptor.Lamda'
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30 --Weight '$SelectDiscriptor.Weight'
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31 #end if
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34 -O '$output1'
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36 ]]></command>
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38 <inputs>
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40 <param name="input1" type="data" format="fasta" label="Input fasta file" help="Input fasta file with peptides"/>
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42 <conditional name="SelectDiscriptor">
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44 <param name="DesType" type="select" label="Descriptor Type" argument="">
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45 <option value="PAAC">PAAC</option>
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46 <option value="APAAC">APAAC</option>
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47 <option value="CTD" selected="true">CTD</option>
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48 <option value="DPComp">DPComp</option>
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49 <option value="GearyAuto">GearyAuto</option>
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50 <option value="MoranAuto">MoranAuto</option>
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51 <option value="MoreauBrotoAuto">MoreauBrotoAuto</option>
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52 <option value="QSO">QSO</option>
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53 <option value="SOCN">SOCN</option>
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54 <option value="TPComp">TPComp</option>
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55 <option value="BinaryDescriptor">Binary Descriptor</option>
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56 <option value="All">All</option>
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57 </param>
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58
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59 <when value="PAAC" >
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60 <param name="Lamda" type="integer" label="Lamda" value="50" argument="--Lamda" help="Lamda"/>
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61 <param name="Weight" type="float" label="Weight" value="0.5" argument="--Weight" help="Weight"/>
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62 </when>
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64 <when value="APAAC" >
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65 <param name="Lamda" type="integer" value="50" argument="--Lamda" help="Lamda"/>
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66 <param name="Weight" type="float" value="0.5" argument="--Weight" help="Weight"/>
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67 </when>
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69 <when value="All" >
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70 <param name="Lamda" type="integer" value="50" label="Lamda" argument="--Lamda" help="Lamda"/>
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71 <param name="Weight" type="float" value="0.5" argument="--Weight" help="Weight"/>
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72 </when>
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74 <when value="DPComp" >
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75 </when>
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77 <when value="GearyAuto" >
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78 </when>
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80 <when value="MoranAuto" >
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81 </when>
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83 <when value="MoreauBrotoAuto" >
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84 </when>
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86 <when value="QSO" >
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87 </when>
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89 <when value="SOCN" >
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90 </when>
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92 <when value="CTD" >
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93 </when>
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95 <when value="TPComp" >
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96 </when>
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98 <when value="BinaryDescriptor" >
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99 </when>
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100
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101
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102 </conditional>
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103
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104 </inputs>
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105
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106 <outputs>
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107 <data name='output1' format='tabular' label="${tool.name} on $on_string - ${SelectDiscriptor.DesType} (tabular)" />
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108 </outputs>
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109
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110 <tests>
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111 <test>
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112 <param name="input1" value="positive.fasta"/>
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113 <param name="DesType" value="All"/>
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114 <param name="Lamda" value="5"/>
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115 <param name="Weight" value="0.5"/>
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116 <output name="output1" value="Out.tsv"/>
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117 </test>
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118
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119
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120 <test>
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121 <param name="input1" value="positive.fasta"/>
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122 <param name="DesType" value="BinaryDescriptor"/>
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123 <output name="output1" value="Out1.tsv"/>
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124 </test>
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125
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126 </tests>
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127 <help><![CDATA[
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128 .. class:: infomark
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129
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130 **What it does**
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131
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132 This tool calculates sequence property based descriptor for a peptide descriptor. 
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133
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134 * **AAC** This option calculates amino acid composition descriptors (20).
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135   * **DPComp** This option calculates dipeptide composition descriptors (400).
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136   * **TPComp** This option calculates tri-peptide composition descriptors (8000).
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137   * **MoreauBrotoAuto** This option calculates Normalized Moreau-Broto autocorrelation descriptors (depend on the given properties, the default is 240).
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138   * **MoranAuto** This option calculates Moran autocorrelation descriptors (depend on the given properties, the default is 240).
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139   * **GearyAuto** This option calculates Geary autocorrelation descriptors (depend on the given properties, the default is 240).
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140   * **CTD** This option calculates Composition, Transition, Distribution descriptors(200).
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141   * **SOCN** This option calculates sequence order coupling numbers (depend on the choice of maxlag, the default is 60).
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142   * **QSO** This option calculates quasi-sequence order descriptors (depend on the choice of maxlag, the default is 100).
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143   * **PAAC** This option calculates pseudo amino acid composition descriptors (depend on the choice of lamda, the default is 50).
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144   * **APAAC** This option calculates amphiphilic pseudo amino acid composition descriptors, (depend on the choice of lamda, the default is 50).
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145   * **BinaryDescriptor** This option calculates the binary descriptor of peptide sequences (All the peptides should be the same length).
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146   * **All** This option calculates all the descriptors except the binary descriptor.
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147
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148 -----
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149
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150 **Inputs**
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151 * **--InFile** A fasta file with peptide sequences.
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152 * **--Lamda** PAAC & APAAC descriptors (depend on the choice of lamda, the default is 50).
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153 * **--Weight** PAAC & APAAC descriptors (depend on the choice of lamda, the default is 0.5).
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154 * **--DesType** Select the descriptor type.
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155
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156
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157 -----
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158
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159 **Outputs**
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160 * Returns tabular file with descriptors.
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161
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162 ]]></help>
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163
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164 <citations>
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165 <citation type="bibtex">
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166 @misc{PDAUGGITHUB,
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167 author = {Joshi, Jayadev and Blankenberg, Daniel},
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168 year = {2020},
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169 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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170 publisher = {GitHub},
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171 journal = {GitHub repository},
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172 url =
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173 {https://github.com/jaidevjoshi83/pdaug.git},
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174 }
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175 </citation>
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176 <citation type="bibtex">
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177 @article{cao_liang_yan_tan_xu_liu_2013,
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178 title={PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies},
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179 volume={53}, DOI={10.1021/ci400127q},
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180 number={11},
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181 journal={Journal of Chemical Information and Modeling},
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182 author={Cao, Dong-Sheng and Liang, Yi-Zeng and Yan, Jun and Tan, Gui-Shan and Xu, Qing-Song and Liu, Shao},
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183 year={2013},
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184 pages={3086–3096}}
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185 </citation>
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186 </citations>
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187 </tool>
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188
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189
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190