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comparison log_and_glog_transformation.xml @ 1:2e7d47c0b027 draft

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"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author malex
date Mon, 08 Mar 2021 22:04:06 +0000
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0:b54326490b4d 1:2e7d47c0b027
1 <tool id="secimtools_log_and_glog_transformation" name="Log and Generalized Log (G-Log) Transformation." version="@WRAPPER_VERSION@">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command><![CDATA[
8 log_and_glog_transformation.py
9 --input $input
10 --design $design
11 --uniqID $uniqID
12 --transformation $transformation
13 --log_base $log_base
14 --lambda_value $lambda_value
15 --oname $oname
16 ]]></command>
17 <inputs>
18 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
19 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
20 <param name="uniqID" size="30" type="text" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers.."/>
21 <param name="transformation" size="30" display="radio" type="select" value="log" label="Select Transformation" help="Select log or G-log.">
22 <option value="log" selected="true">Logarithm</option>
23 <option value="glog" selected="true">Generalized Logarithm (G-Log)</option>
24 </param>
25 <param name="log_base" size="30" type="select" display="radio" value="log" label="Logarithm Base" help="Select logarithm base.">
26 <option value="log" selected="true">Logarithm base e (natural)</option>
27 <option value="log2" selected="true">Logarithm base 2</option>
28 <option value="log10" selected="true">Logarithm base 10</option>
29 </param>
30 <param name="lambda_value" size="30" type="text" value="100" label="Regularization Parameter Lambda" help='Regularization parameter lambda is used only for G-log transformation and is ignored for log transformation. Lambda must be non-negative.'/>
31 </inputs>
32 <outputs>
33 <data format="tabular" name="oname" label="${tool.name} on ${on_string}" />
34 </outputs>
35 <tests>
36 <test>
37 <param name="input" value="ST000006_data.tsv"/>
38 <param name="design" value="ST000006_design.tsv"/>
39 <param name="uniqID" value="Retention_Index" />
40 <param name="transformation" value="glog" />
41 <param name="log_base" value="log" />
42 <param name="lambda_value" value="1000000" />
43 <output name="oname" file="ST000006_log_and_glog_transformation_glog_lambda_1000000.tsv" />
44 </test>
45 <test>
46 <param name="input" value="ST000006_data.tsv"/>
47 <param name="design" value="ST000006_design.tsv"/>
48 <param name="uniqID" value="Retention_Index" />
49 <param name="transformation" value="log" />
50 <param name="log_base" value="log" />
51 <param name="lambda_value" value="0" />
52 <output name="oname" file="ST000006_log_and_glog_transformation_log.tsv" />
53 </test>
54 </tests>
55 <help><![CDATA[
56
57 @TIP_AND_WARNING@
58
59 **Tool Description**
60
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.***
62
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.
64
65 The logarithmic transformation has the formula: log(data).
66
67 The generalized logarithmic transformation has the formula: log(data + sqrt(data^2 + lambda)).
68
69 The generalized version becomes the standard logarithmic transformation re-scaled by sqrt(2) if the lambda value is 0.
70
71 Three bases are available for both logarithmic transformations:
72
73 base e (natural), base 2, and base 10.
74
75
76
77 --------------------------------------------------------------------------------
78
79 **Input**
80
81 - Two input datasets are required.
82
83 @WIDE@
84
85 **NOTE:** The sample IDs must match the sample IDs in the Design File (below).
86 Extra columns will automatically be ignored.
87
88 @METADATA@
89
90 @UNIQID@
91
92 **Transformation Choice**
93
94 - User has to choose between logarithmic and generalized logarithmic (G-log) transformation.
95
96 **Logarithm Base**
97
98 - Select base of the logarithm.
99
100 **Regularization Parameter Lambda**
101
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.
103
104 --------------------------------------------------------------------------------
105
106 **Output**
107
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.
109
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.
111 Any values missing in the original dataset will remain missing.
112
113 ]]></help>
114 <expand macro="citations"/>
115 </tool>