Mercurial > repos > malex > secimtools
diff log_and_glog_transformation.xml @ 1:2e7d47c0b027 draft
"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author | malex |
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date | Mon, 08 Mar 2021 22:04:06 +0000 |
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children | caba07f41453 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/log_and_glog_transformation.xml Mon Mar 08 22:04:06 2021 +0000 @@ -0,0 +1,115 @@ +<tool id="secimtools_log_and_glog_transformation" name="Log and Generalized Log (G-Log) Transformation." version="@WRAPPER_VERSION@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command><![CDATA[ +log_and_glog_transformation.py +--input $input +--design $design +--uniqID $uniqID +--transformation $transformation +--log_base $log_base +--lambda_value $lambda_value +--oname $oname + ]]></command> + <inputs> + <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/> + <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/> + <param name="uniqID" size="30" type="text" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers.."/> + <param name="transformation" size="30" display="radio" type="select" value="log" label="Select Transformation" help="Select log or G-log."> + <option value="log" selected="true">Logarithm</option> + <option value="glog" selected="true">Generalized Logarithm (G-Log)</option> + </param> + <param name="log_base" size="30" type="select" display="radio" value="log" label="Logarithm Base" help="Select logarithm base."> + <option value="log" selected="true">Logarithm base e (natural)</option> + <option value="log2" selected="true">Logarithm base 2</option> + <option value="log10" selected="true">Logarithm base 10</option> + </param> + <param name="lambda_value" size="30" type="text" value="100" label="Regularization Parameter Lambda" help='Regularization parameter lambda is used only for G-log transformation and is ignored for log transformation. Lambda must be non-negative.'/> + </inputs> + <outputs> + <data format="tabular" name="oname" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input" value="ST000006_data.tsv"/> + <param name="design" value="ST000006_design.tsv"/> + <param name="uniqID" value="Retention_Index" /> + <param name="transformation" value="glog" /> + <param name="log_base" value="log" /> + <param name="lambda_value" value="1000000" /> + <output name="oname" file="ST000006_log_and_glog_transformation_glog_lambda_1000000.tsv" /> + </test> + <test> + <param name="input" value="ST000006_data.tsv"/> + <param name="design" value="ST000006_design.tsv"/> + <param name="uniqID" value="Retention_Index" /> + <param name="transformation" value="log" /> + <param name="log_base" value="log" /> + <param name="lambda_value" value="0" /> + <output name="oname" file="ST000006_log_and_glog_transformation_log.tsv" /> + </test> + </tests> + <help><![CDATA[ + +@TIP_AND_WARNING@ + +**Tool Description** + +***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.*** + +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. + +The logarithmic transformation has the formula: log(data). + +The generalized logarithmic transformation has the formula: log(data + sqrt(data^2 + lambda)). + +The generalized version becomes the standard logarithmic transformation re-scaled by sqrt(2) if the lambda value is 0. + +Three bases are available for both logarithmic transformations: + +base e (natural), base 2, and base 10. + + + +-------------------------------------------------------------------------------- + +**Input** + + - Two input datasets are required. + +@WIDE@ + +**NOTE:** The sample IDs must match the sample IDs in the Design File (below). +Extra columns will automatically be ignored. + +@METADATA@ + +@UNIQID@ + +**Transformation Choice** + + - User has to choose between logarithmic and generalized logarithmic (G-log) transformation. + +**Logarithm Base** + + - Select base of the logarithm. + +**Regularization Parameter Lambda** + + - Enter a value for regularization parameter lambda. The value must to be non-negative and is used only for G-log transformation. Default = 100. + +-------------------------------------------------------------------------------- + +**Output** + +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. + +***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. +Any values missing in the original dataset will remain missing. + + ]]></help> + <expand macro="citations"/> +</tool>