--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/waveica.xml	Thu Mar 18 15:53:38 2021 +0000
@@ -0,0 +1,133 @@
+<tool id="waveica" name="WaveICA" version="0.1.0+galaxy0" python_template_version="3.5">
+
+    <description>removal of batch effects for untargeted metabolomics data</description>
+    
+    <requirements>
+        <container type="docker">recetox/waveica:0.1.0-recetox0</container>
+    </requirements>
+
+    <command detect_errors="aggressive"><![CDATA[
+        Rscript
+            -e 'source("${__tool_directory__}/waveica_wrapper.R")'
+
+            -e 'normalized_data <- waveica(
+                data = "$data",
+                wavelet_filter = "$parameters.wf.wavelet_filter",
+                wavelet_length = "$parameters.wf.wavelet_length",
+                k = $parameters.k,
+                t = $parameters.t,
+                t2 = $parameters.t2,
+                alpha = $parameters.alpha,
+                exclude_blanks = $optional_parameters.exclude_blanks
+            )'
+
+            -e 'store_data(normalized_data,"$normalized_features")'
+    ]]></command>
+
+    <inputs>
+        <param type="data" name="data" label="Sample-by-matrix data" format="csv" help=""/>
+        <section name="parameters" title="Normalization Parameters" expanded="True">
+            <conditional name="wf">
+                <param type="select" name="wavelet_filter" label="Wavelet transform filter" help="selecting wavelet function and filter length">
+                    <option value="d" selected="True">Daubechies</option>
+                    <option value="la" >Least Asymetric</option>
+                    <option value="bl" >Best Localized</option>
+                    <option value="c" >Coiflet</option>
+                </param>
+                <when value="d">
+                    <param name="wavelet_length" type="select" label="filter length">
+                        <option value="2" selected="True">2</option>
+                        <option value="4">4</option>
+                        <option value="6">6</option>
+                        <option value="8">8</option>
+                        <option value="10">10</option>
+                        <option value="12">12</option>
+                        <option value="14">14</option>
+                        <option value="16">16</option>
+                        <option value="18">18</option>
+                        <option value="20">20</option>
+                    </param>
+                </when>
+                <when value="la">
+                    <param name="wavelet_length" type="select" label="filter length">
+                        <option value="8">8</option>
+                        <option value="10">10</option>
+                        <option value="12">12</option>
+                        <option value="14">14</option>
+                        <option value="16">16</option>
+                        <option value="18">18</option>
+                        <option value="20">20</option>
+                    </param>
+                </when>
+                <when value="bl">
+                    <param name="wavelet_length" type="select" label="filter length">
+                        <option value="14">14</option>
+                        <option value="18">18</option>
+                        <option value="20">20</option>
+                    </param>
+                </when>
+                <when value="c">
+                    <param name="wavelet_length" type="select" label="filter length">
+                        <option value="6">6</option>
+                        <option value="12">12</option>
+                        <option value="18">18</option>
+                        <option value="24">24</option>
+                        <option value="30">30</option>
+                    </param>
+                </when>
+            </conditional>
+            <param type="integer" value="20" name="k" label="Number of components to decompose" help="the maximal component that ICA decomposes"/>
+            <param type="float" value="0.05" name="t" label="Batch-assosiation threshold" help="the threshold to consider a component associate with the batch,
+ should be between 0 and 1"/>
+            <param type="float" value="0.05" name="t2" label="Group-assosiation threshold" help="the threshold to consider a component associate with the group,
+ should be between 0 and 1"/>
+            <param type="float" value="0" name="alpha" label="Alpha" help="the trade-off value between the independence of samples and those of variables and should be between 0 and 1"/>
+        </section>
+        <section name="optional_parameters" expanded="true" title="Optional Parameters">
+            <param name="exclude_blanks" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" />
+        </section>
+    </inputs>
+
+    <outputs>
+        <data name="normalized_features" format="tsv" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="data" value="features-test.csv" ftype="csv" />
+            <param name="wavelet_filter" value="d" />
+            <param name="filter_length" value="2" />
+            <param name="k" value="20" />
+            <param name="t" value="0.05" />
+            <param name="t2" value="0.05" />
+            <param name="alpha" value="0" />
+            <output name="normalized_features" file="features-normalized.tsv" /> 
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        **Description**
+
+        Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis. The WaveICA R package provides a new algorithm to removing batch effects for metabolomics data.
+        
+        The input is Sample-by-matrix table which must include: 
+
+        1. Injection order of samples
+
+        2. Types of the samples denoted as "blank", "sample" or "QC"
+
+        3. Batch numbers
+
+        4. Features data
+
+        **Documentation**
+
+        See original repository for further information: https://github.com/dengkuistat/WaveICA
+
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1016/j.aca.2019.02.010</citation>
+    </citations>
+
+</tool>
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