--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/secimtools/log_and_glog_transformation.xml	Mon Mar 08 20:55:03 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>