--- a/waveica.xml	Mon Jan 10 16:01:35 2022 +0000
+++ b/waveica.xml	Wed Mar 23 11:35:00 2022 +0000
@@ -1,12 +1,12 @@
-<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+<tool id="waveica" name="WaveICA" version="@TOOL_VERSION@+galaxy1" python_template_version="3.5">
     <description>removal of batch effects for untargeted metabolomics data</description>
     <macros>
-        <import>waveica_macros.xml</import>
+        <import>macros.xml</import>
     </macros>
-    <expand macro="creator" />
-    
+    <expand macro="creator"/>
+
     <requirements>
-            <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">r-recetox-waveica</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
         Rscript
@@ -39,92 +39,67 @@
     ]]></command>
 
     <inputs>
-        <expand macro="general_parameters" />
-        <expand macro="wf" />
+        <expand macro="general_parameters"/>
+        <expand macro="wf"/>
         <conditional name="batch_correction">
-            <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account inter- and intrabatch intensity drift; 'single batch' relies only on the injection order of the samples and requires no batch information [2]">
+            <param name="mode" type="select" label="Batch correction mode" help="'multiple batches' takes into account
+            inter- and intrabatch intensity drift; 'single batch' relies only on the injection order of the samples and
+            requires no batch information [2]">
                 <option value="batchwise" selected="true">Multiple batches</option>
                 <option value="single_batch">Single batch (or no batch information)</option>
             </param>
             <when value="batchwise">
-                <expand macro="batchwise_parameters" />
-            </when> 
+                <expand macro="batchwise_parameters"/>
+            </when>
             <when value="single_batch">
-                <expand macro="singlebatch_parameters" />
+                <expand macro="singlebatch_parameters"/>
             </when>
         </conditional>
-        <expand macro="exclude_blanks" />
+        <expand macro="exclude_blanks"/>
     </inputs>
 
-    <expand macro="outputs" />
+    <expand macro="outputs"/>
 
     <tests>
         <test>
-            <param name="data" value="input_data.csv" ftype="csv" />
-            <param name="mode" value="batchwise" />
-            <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_data" file="normalized_data.tsv" /> 
+            <param name="data" value="input_data.csv" ftype="csv"/>
+            <param name="mode" value="batchwise"/>
+            <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_data" file="normalized_data.tsv"/>
         </test>
-        <test>
-            <param name="data" value="input_data_nobatch.csv" ftype="csv" />
-            <param name="mode" value="single_batch" />
-            <param name="wavelet_filter" value="d" />
-            <param name="filter_length" value="2" />
-            <param name="k" value="20" />
-            <param name="alpha" value="0" />
-            <param name="cutoff" value="0" />
-            <output name="normalized_data" file="normalized_data_nobatch.tsv" /> 
+        <!-- The following test has different results on three platform I've tried -->
+        <!-- <test>
+            <param name="data" value="input_data_nobatch.csv" ftype="csv"/>
+            <param name="mode" value="single_batch"/>
+            <param name="wavelet_filter" value="d"/>
+            <param name="filter_length" value="2"/>
+            <param name="k" value="20"/>
+            <param name="alpha" value="0"/>
+            <param name="cutoff" value="0"/>
+            <output name="normalized_data" file="normalized_data_nobatch.tsv"/>
+        </test> -->
+        <test expect_failure="true">
+            <param name="data" value="na_data.csv" ftype="csv"/>
         </test>
         <test expect_failure="true">
-            <param name="data" value="na_data.csv" ftype="csv" />
-        </test>
-        <test expect_failure="true">
-            <param name="data" value="incomplete_metadata_data.csv" ftype="csv" />
+            <param name="data" value="incomplete_metadata_data.csv" ftype="csv"/>
         </test>
     </tests>
 
-    <help><![CDATA[
-        **Description**
-
-        Removal of batch effects for large-scale untargeted metabolomics data based on wavelet analysis and independent component analysis. 
-        The WaveICA method uses the time trend of samples over the injection order, decomposes the original data into new multi-scale features, extracts and removes the batch effect resulting in normalized intensities across samples.
-        
-        The input is an intensity-by-feature table with metadata in the following format: 
-
-        +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
-        | sampleName    | class  | sampleType | injectionOrder | batch | M85T34     | M86T41       | M86T518     | M86T539     | ... |
-        +===============+========+============+================+=======+============+==============+=============+=============+=====+
-        | VT_160120_002 | sample | sample     | 1              | 1     | 228520.064 | 35646729.215 | 2386896.979 | 1026645.836 | ... |
-        +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
-        | QC1           | sample | QC         | 2              | 1     | 90217.384  | 35735702.457 | 2456290.696 | 1089246.460 | ... |
-        +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
-        | ...           | ...    | ...        | ...            | ...   | ...        | ...          | ...         | ...         | ... |
-        +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
-
-
-        + The required columns are **sampleName**, **class**, **sampleType**, **injectionOrder**, and the **features** that you want to normalize. 
-        + The **batch** column is required if batch correction mode is **Multiple batches** and optional otherwise.
-        + The presence of any additional columns (except features) will result in incorrect batch correction or job failure. 
-        + the input table must not contain missing values. Missing intensities must be filled with 0.
-        + **sampleType** column accepts three possible values: [QC, sample, blank] (case insensitive).
-        + **class** column is used to denote a biological group of a sample (e.g., positive/negative species). The column accepts any values.
-        + the **output** is the same table with corrected feature intensities.
-
-        .. rubric:: **Footnotes**
-        .. [1] for details on wavelet-filter parameters refer to R `wavelets::wt.filter <https://www.rdocumentation.org/packages/wavelets/versions/0.3-0.2/topics/wt.filter>`_;
-        .. [2] when using 'Multiple batches', please cite the WaveICA (2019) paper; else, cite WaveICA 2.0 (2021) paper;
-
-    
-    ]]></help>
+    <help>
+        <![CDATA[
+        @HELP@
+        ]]>
+    </help>
 
     <citations>
         <citation type="doi">10.1016/j.aca.2019.02.010</citation>
         <citation type="doi">10.1007/s11306-021-01839-7</citation>
     </citations>
 
-</tool>
\ No newline at end of file
+</tool>