Mercurial > repos > jay > pdaug_sequence_property_based_descriptors
annotate PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.xml @ 0:6b6aec52638d draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:23:51 +0000 |
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children | 7dc979925e31 |
rev | line source |
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0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 <tool id="pdaug_sequence_property_based_descriptors" name="PDAUG Sequence Property Based Descriptors" version="0.1.0"> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 <description>Calculates sequence based descriptors of the peptide sequences</description> |
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3 |
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4 <requirements> |
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5 <requirement type="package" version="2.7.18">python</requirement> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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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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13 |
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14 python '$__tool_directory__/PDAUG_Sequence_Property_Based_Descriptors.py' --InFile '$input1' |
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15 |
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16 --DesType '$SelectDiscriptor.DesType' |
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17 |
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18 #if '$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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22 |
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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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27 |
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28 #if $SelectDiscriptor.DesType == 'All' |
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29 --Lamda '$SelectDiscriptor.Lamda' |
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30 --Weight '$SelectDiscriptor.Weight' |
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31 #end if |
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32 |
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33 |
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34 -O '$output1' |
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35 |
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36 ]]></command> |
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37 |
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38 <inputs> |
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39 |
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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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41 |
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42 <conditional name="SelectDiscriptor"> |
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43 |
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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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63 |
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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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68 |
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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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73 |
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74 <when value="DPComp" > |
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75 </when> |
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76 |
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77 <when value="GearyAuto" > |
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78 </when> |
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79 |
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80 <when value="MoranAuto" > |
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81 </when> |
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82 |
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83 <when value="MoreauBrotoAuto" > |
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84 </when> |
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85 |
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86 <when value="QSO" > |
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87 </when> |
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88 |
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89 <when value="SOCN" > |
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90 </when> |
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91 |
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92 <when value="CTD" > |
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93 </when> |
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94 |
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95 <when value="TPComp" > |
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96 </when> |
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97 |
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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 |