diff macros.xml @ 0:328710890963 draft

"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/waveica commit 98e541a75678eee749261630610b946c258fd5f3"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Mar 23 11:35:30 2022 +0000
@@ -0,0 +1,127 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.2.0</token>
+
+    <xml name="creator">
+        <creator>
+            <person
+                givenName="Maksym"
+                familyName="Skoryk"
+                url="https://github.com/maximskorik"
+                identifier="0000-0003-2056-8018" />
+            <organization
+                url="https://www.recetox.muni.cz/"
+                email="[e-mail]"
+                name="RECETOX MUNI" />
+        </creator>
+    </xml>
+
+    <xml name="general_parameters">
+        <param type="data" name="data" label="Feature table" format="csv" help=""/>
+        <param type="integer" value="20" name="k" label="Number of components to decompose" help="maximal component that ICA decomposes"/>
+        <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"/>
+    </xml>
+    <xml name="batchwise_parameters">
+        <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-association threshold" help="threshold to consider a component associate with the group,
+        should be between 0 and 1"/>
+    </xml>
+    <xml name="singlebatch_parameters">
+        <param type="float" value="0" name="cutoff" label="Cutoff" help="threshold of the variation explained by the injection order for independent components, should be between 0 and 1"/>
+    </xml>
+    <xml name="exclude_blanks">
+        <param name="exclude_blanks" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Remove blanks" help="Excludes blank samples from the output" />
+    </xml>
+    <xml name="wf">
+        <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>
+            <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>
+    </xml>
+
+    <xml name="outputs">
+        <outputs>
+            <data name="normalized_data" format="tsv" />
+        </outputs>
+    </xml>
+
+    <token name="@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;
+    ]]>
+    </token>
+</macros>