Mercurial > repos > jay > pdaug_sequence_property_based_descriptors

annotate PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.xml @ 5:7dc979925e31 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
author jay
date Thu, 28 Jan 2021 04:18:51 +0000
parents 6b6aec52638d
children dd4523d4ae2f
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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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10 <command detect_errors="exit_code"><![CDATA[
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12 python '$__tool_directory__/PDAUG_Sequence_Property_Based_Descriptors.py' --InFile '$input1'
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14 --DesType '$SelectDiscriptor.DesType'
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17 #if $SelectDiscriptor.DesType == 'GetPAAC'
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19 --Lamda '$SelectDiscriptor.Lamda'
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20 --Weight '$SelectDiscriptor.Weight'
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22 #end if
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25 #if $SelectDiscriptor.DesType == 'GetAPAAC'
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27 --Lamda '$SelectDiscriptor.Lamda'
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28 --Weight '$SelectDiscriptor.Weight'
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30 #end if
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33 #if $SelectDiscriptor.DesType == 'GetSOCN'
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35 --MaxLag '$SelectDiscriptor.MaxLag'
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37 #end if
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40 #if $SelectDiscriptor.DesType =='GetQSO'
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42 --MaxLag '$SelectDiscriptor.MaxLag'
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43 --Weight '$SelectDiscriptor.Weight'
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45 #end if
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48 #if $SelectDiscriptor.DesType =='All'
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50 --MaxLag '$SelectDiscriptor.MaxLag'
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51 --Weight '$SelectDiscriptor.Weight'
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52 --Lamda '$SelectDiscriptor.Lamda'
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54 #end if
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58 -O '$output1'
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60 ]]></command>
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62 <inputs>
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64 <param name="input1" type="data" format="fasta" label="Input fasta file" help="Input fasta file with peptides"/>
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66 <conditional name="SelectDiscriptor">
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68 <param name="DesType" type="select" label="Descriptor Type" argument="">
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69 <option value="GetAAComp">GetAAComp</option>
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70 <option value="GetDPComp">GetDPComp</option>
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71 <option value="GetTPComp" selected="true">GetTPComp</option>
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72 <option value="GetMoreauBrotoAuto">GetMoreauBrotoAuto</option>
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73 <option value="GetMoranAuto">GetMoranAuto</option>
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74 <option value="GetGearyAuto">GetGearyAuto</option>
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75 <option value="GetCTD">GetCTD</option>
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76 <option value="GetPAAC">GetPAAC</option>
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77 <option value="GetAPAAC">GetAPAAC</option>
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78 <option value="GetSOCN">GetSOCN</option>
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79 <option value="GetQSO">GetQSO</option>
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80 <option value="GetTriad">GetTriad</option>
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81 <option value="BinaryDescriptor">Binary Descriptor</option>
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82 <option value="All">All</option>
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83 </param>
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84
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85 <when value="GetPAAC" >
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86 <param name="Lamda" type="integer" label="Lamda" value="10" help="A non negative integer"/>
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87 <param name="Weight" type="float" label="Weight" value="0.5" help="Any value within the range from 0.05 to 0.7"/>
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88 </when>
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89
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90 <when value="GetAPAAC" >
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91 <param name="Lamda" type="integer" label="Lamda" value="10" help="A non negative integer"/>
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92 <param name="Weight" type="float" label="Weight" value="0.5" help="Any value within the range from 0.05 to 0.7"/>
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93 </when>
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95 <when value="GetQSO">
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96 <param name="MaxLag" type="integer" label="MaxLag" value="10" help="A non negative integer"/>
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97 <param name="Weight" type="float" label="Weight" value="0.5" help="Any value within the range from 0.05 to 0.7"/>
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98 </when>
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99
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100 <when value="GetSOCN">
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101 <param name="MaxLag" type="integer" label="MaxLag" value="10" help="A non negative integer"/>
0
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102 </when>
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103
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104 <when value="All" >
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105 <param name="Lamda" type="integer" value="10" label="Lamda" help="A non negative integer"/>
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106 <param name="Weight" type="float" value="0.5" label="Weight" help="Weight"/>
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107 <param name="MaxLag" type="integer" value="10" label="Lamda" help="A non negative integer"/>
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108 </when>
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109
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110 <when value="GetAAComp" >
0
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111 </when>
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112
5
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113 <when value="GetDPComp" >
0
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114 </when>
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115
5
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116 <when value="GetTPComp" >
0
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117 </when>
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118
5
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119 <when value="GetMoreauBrotoAuto" >
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120 </when>
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121
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122 <when value="GetGearyAuto" >
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123 </when>
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124
5
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125 <when value="GetCTD" >
0
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126 </when>
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127
5
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128 <when value="GetPAAC" >
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129 </when>
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130
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131 <when value="GetAPAAC" >
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132 </when>
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133
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134 <when value="GetSOCN">
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135 </when>
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136
5
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137 <when value="GetQSO">
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138 </when>
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139
5
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140 <when value="GetTriad">
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141 </when>
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142
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143 <when value="GetMoranAuto">
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144 </when>
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145
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146 <when value="BinaryDescriptor" >
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147 </when>
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148
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149 </conditional>
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150
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151 </inputs>
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152
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153 <outputs>
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154 <data name='output1' format='tabular' label="${tool.name} on $on_string - ${SelectDiscriptor.DesType} (tabular)" />
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155 </outputs>
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156
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157 <tests>
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158 <test>
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159 <param name="input1" value="positive.fasta"/>
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160 <param name="DesType" value="All"/>
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161 <param name="Lamda" value="10"/>
0
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162 <param name="Weight" value="0.5"/>
5
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163 <param name="MaxLag" value="10"/>
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164 <output name="output1" value="Out.tsv"/>
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165 </test>
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166
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167
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168 <test>
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169 <param name="input1" value="positive.fasta"/>
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170 <param name="DesType" value="BinaryDescriptor"/>
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171 <output name="output1" value="Out1.tsv"/>
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172 </test>
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173
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174 </tests>
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175 <help><![CDATA[
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176 .. class:: infomark
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177
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178 **What it does**
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179
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180 This tool calculates sequence property based descriptor for a peptide descriptor. 
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181
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182 * **GetAAComp** Amino acid compositon descriptors.
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183 * **GetDPComp** Dipeptide composition descriptors.
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184 * **GetTPComp** Tri-peptide composition descriptors.
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185 * **GetMoreauBrotoAuto** Normalized Moreau-Broto autocorrelation descriptors.
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186 * **GetMoranAuto** Moran autocorrelation descriptors.
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187 * **GetGearyAuto** Geary autocorrelation descriptors.
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188 * **GetCTD** Composition Transition Distribution descriptors.
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189 * **GetPAAC** Type I Pseudo amino acid composition descriptors.
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190 * **GetAPAAC** Amphiphilic (Type II) Pseudo amino acid composition descriptors.
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191 * **GetSOCN** Sequence order coupling numbers.
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192 * **GetQSO** Quasi sequence order descriptors default is 10, maxlag is the maximum lag. (The length of the protein should be larger than maxlag).
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193 * **GetTriad** Calculate the conjoint triad features from the protein sequence.
0
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194
5
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195 **Inputes**
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196
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197 * **Input fasta file** Fasta file with peptide sequences.
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198 * **Lamda** lamda reflects the rank of correlation, must be a non-Negative integer. Lamda should NOT be larger than the length of the input protein sequence.
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199 * **Weight** weight is designed for the users to put weight on the additional PseAA components. Any value within the range from 0.05 to 0.7 for the weight factor can be used.
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200 * **Maxlag** maxlag is the maximum lag. a non negative integer. The length of the protein should be larger than maxlag.
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201
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202 -----
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203
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204 **Outputs**
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205 * Returns tabular file with descriptors.
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206
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207 ]]></help>
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208
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209 <citations>
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210 <citation type="bibtex">
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211 @misc{PDAUGGITHUB,
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212 author = {Joshi, Jayadev and Blankenberg, Daniel},
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213 year = {2020},
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214 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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215 publisher = {GitHub},
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216 journal = {GitHub repository},
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217 url =
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218 {https://github.com/jaidevjoshi83/pdaug.git},
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219 }
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220 </citation>
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221 <citation type="bibtex">
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222 @article{cao_liang_yan_tan_xu_liu_2013,
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223 title={PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies},
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224 volume={53}, DOI={10.1021/ci400127q},
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225 number={11},
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226 journal={Journal of Chemical Information and Modeling},
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227 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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228 year={2013},
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229 pages={3086–3096}}
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230 </citation>
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231 </citations>
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232 </tool>
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233
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234
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235