--- a/waveica.xml	Wed Jul 28 11:58:20 2021 +0000
+++ b/waveica.xml	Fri Nov 12 09:14:04 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="waveica" name="WaveICA" version="0.1.0+galaxy1" python_template_version="3.5">
+<tool id="waveica" name="WaveICA" version="0.1.0+galaxy2" python_template_version="3.5">
 
     <description>removal of batch effects for untargeted metabolomics data</description>
     
@@ -12,96 +12,98 @@
 
             -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 = $optional_parameters.exclude_blanks
+                wavelet_filter = "$wf.wavelet_filter",
+                wavelet_length = "$wf.wavelet_length",
+                k = $k,
+                t = $t,
+                t2 = $t2,
+                alpha = $alpha,
+                exclude_blanks = $exclude_blanks
             )'
 
-            -e 'store_data(normalized_data,"$normalized_features")'
+            -e 'store_data(normalized_data,"$normalized_data")'
     ]]></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 type="data" name="data" label="Feature table" format="csv" help=""/>
+        <conditional name="wf">
+            <param type="select" name="wavelet_filter" label="Wavelet transform filter" help="wavelet function and filter length [1] (see footnotes for more details)">
+                <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 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,
+            </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="maximal component that ICA decomposes"/>
+        <param type="float" value="0.05" name="t" label="Batch-association threshold" help="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,
+        <param type="float" value="0.05" name="t2" label="Group-association threshold" help="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>
+        <param type="float" value="0" name="alpha" label="Alpha" help="trade-off value between the independence of samples (temporal ICA) and variables (spatial ICA), should be between 0 and 1"/>
+        <param name="exclude_blanks" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" />
     </inputs>
 
     <outputs>
-        <data name="normalized_features" format="tsv" />
+        <data name="normalized_data" format="tsv" />
     </outputs>
 
     <tests>
         <test>
-            <param name="data" value="features-test.csv" ftype="csv" />
+            <param name="data" value="input_data.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" /> 
+            <output name="normalized_data" file="normalized_data.tsv" /> 
+        </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" />
         </test>
     </tests>
 
@@ -110,19 +112,26 @@
 
         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"
+        The input is an intensity-by-feature table with metadata in the following format: 
 
-        3. Batch numbers
-
-        4. Features data
+        +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
+        | 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 | ... |
+        +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
+        | ...           | ...    | ...        | ...            | ...   | ...        | ...          | ...         | ...         | ... |
+        +---------------+--------+------------+----------------+-------+------------+--------------+-------------+-------------+-----+
 
-        **Documentation**
 
-        See original repository for further information: https://github.com/dengkuistat/WaveICA
+        + 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>`_;
 
     ]]></help>