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1 <tool id="secimtools_log_and_glog_transformation" name="Log and Generalized Log (G-Log) Transformation." version="@WRAPPER_VERSION@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command><![CDATA[
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8 log_and_glog_transformation.py
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9 --input $input
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10 --design $design
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11 --uniqID $uniqID
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12 --transformation $transformation
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13 --log_base $log_base
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14 --lambda_value $lambda_value
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15 --oname $oname
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16 ]]></command>
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17 <inputs>
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18 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
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19 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
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20 <param name="uniqID" size="30" type="text" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers.."/>
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21 <param name="transformation" size="30" display="radio" type="select" value="log" label="Select Transformation" help="Select log or G-log.">
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22 <option value="log" selected="true">Logarithm</option>
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23 <option value="glog" selected="true">Generalized Logarithm (G-Log)</option>
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24 </param>
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25 <param name="log_base" size="30" type="select" display="radio" value="log" label="Logarithm Base" help="Select logarithm base.">
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26 <option value="log" selected="true">Logarithm base e (natural)</option>
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27 <option value="log2" selected="true">Logarithm base 2</option>
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28 <option value="log10" selected="true">Logarithm base 10</option>
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29 </param>
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30 <param name="lambda_value" size="30" type="text" value="100" label="Regularization Parameter Lambda" help='Regularization parameter lambda is used only for G-log transformation and is ignored for log transformation. Lambda must be non-negative.'/>
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31 </inputs>
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32 <outputs>
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33 <data format="tabular" name="oname" label="${tool.name} on ${on_string}" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input" value="ST000006_data.tsv"/>
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38 <param name="design" value="ST000006_design.tsv"/>
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39 <param name="uniqID" value="Retention_Index" />
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40 <param name="transformation" value="glog" />
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41 <param name="log_base" value="log" />
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42 <param name="lambda_value" value="1000000" />
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43 <output name="oname" file="ST000006_log_and_glog_transformation_glog_lambda_1000000.tsv" />
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44 </test>
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45 <test>
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46 <param name="input" value="ST000006_data.tsv"/>
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47 <param name="design" value="ST000006_design.tsv"/>
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48 <param name="uniqID" value="Retention_Index" />
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49 <param name="transformation" value="log" />
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50 <param name="log_base" value="log" />
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51 <param name="lambda_value" value="0" />
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52 <output name="oname" file="ST000006_log_and_glog_transformation_log.tsv" />
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56
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57 @TIP_AND_WARNING@
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58
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59 **Tool Description**
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60
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61 ***NOTE: Zero or negative values in the original dataset will be replaced with missing values after log transformation since logarithms are not defined for non-positive values.***
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62
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63 This tool carries out either log or generalized log (G-log) transformation of values in a Wide Format dataset using the base specified by the user.
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64
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65 The logarithmic transformation has the formula: log(data).
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66
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67 The generalized logarithmic transformation has the formula: log(data + sqrt(data^2 + lambda)).
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68
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69 The generalized version becomes the standard logarithmic transformation re-scaled by sqrt(2) if the lambda value is 0.
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70
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71 Three bases are available for both logarithmic transformations:
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72
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73 base e (natural), base 2, and base 10.
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74
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75
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76
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77 --------------------------------------------------------------------------------
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78
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79 **Input**
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80
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81 - Two input datasets are required.
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82
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83 @WIDE@
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84
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85 **NOTE:** The sample IDs must match the sample IDs in the Design File (below).
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86 Extra columns will automatically be ignored.
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87
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88 @METADATA@
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89
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90 @UNIQID@
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91
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92 **Transformation Choice**
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93
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94 - User has to choose between logarithmic and generalized logarithmic (G-log) transformation.
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95
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96 **Logarithm Base**
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97
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98 - Select base of the logarithm.
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99
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100 **Regularization Parameter Lambda**
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101
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102 - Enter a value for regularization parameter lambda. The value must to be non-negative and is used only for G-log transformation. Default = 100.
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103
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104 --------------------------------------------------------------------------------
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105
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106 **Output**
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107
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108 A TSV file containing the same column names as the original Wide Dataset where the values in each cell correspond to the values obtained by the selected log transformation procedure.
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109
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110 ***NOTE:*** If the original dataset contains 0 or negative values, they will be replaced with missing values after log transformation since logarithms are not defined for non-positive values.
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111 Any values missing in the original dataset will remain missing.
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112
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113 ]]></help>
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114 <expand macro="citations"/>
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115 </tool>
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