annotate help.xml @ 1:ebb0730f6175 draft default tip

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools commit 91d32d5b671c523cbe1f47cde279cd8d61826c78

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recetox-boxplot help
=====================

Overview
--------

recetox-boxplot tool can be used to plot boxplots for the tabular data. On the input, a dataframe in tabular/csv/parquet format, containing only columns to be plotted (the pre-filtering can be achieved e.g. using the `Cut` Galaxy tool) is expected. If the data contains as the first column the rownames - meaning identificators, ProteinID, etc., please do set the `Does the first column of input table contain rownames?` to TRUE.  

Typically, a table where rows are features and columns are samples is expected - if one wishes to plot the boxplots for the features, we recommend to transpose the table beforehand.

Sometimes, it is better to transform the data for the visualization (or processing) purposes (`Should the quantitative variable be transformed?`). If no transformation option is selected, the data will be plotted as it is. Otherwise, one can choose from replacing all zero values by NA, log2 transformation or log10 transformation. Please note, that NA values are omitted while plotting.

`Plot the boxplots horizontally?` option means flipping the axes: a categorical variable (e.g. samples) would be on y-axis, whereas quantitative variable (e.g. intensity) would be on x-axis. This improves the legibility in case of larger datasets.

It is possible to use also a different variable for the plotting and coloring - in that case, a metadata table (in a tabular format) can be supplied. The metadata table must contain a column which will map to the data table column names (e.g. SampleName). 

It is also possible to use faceting, meaning splitting the plot based on multiple variables. One can then choose which variable to split the x axis and y axis on.

Example data table
-------------------

+----------------------+-------------------+-----------------------+--------------------+
| RowID                |    sample1        |    sample2            |    sample3         |
+======================+===================+=======================+====================+
| 1                    |    350.58         |    211.33             |    288.90          |
+----------------------+-------------------+-----------------------+--------------------+
| 2                    |    130.17         |    287.54             |    100.11          |
+----------------------+-------------------+-----------------------+--------------------+
| 3                    |    134.80         |    683.15             |    112.34          |
+----------------------+-------------------+-----------------------+--------------------+
| 4                    |    183.99         |    920.57             |    590.44          |
+----------------------+-------------------+-----------------------+--------------------+
| ...                  |    ...            |    ...                |    ...             |
+----------------------+-------------------+-----------------------+--------------------+


Example metadata table
-----------------------

+----------------------+-------------------+-----------------------+--------------------+
| SampleName           |    replicate      |    condition          |    batch           |
+======================+===================+=======================+====================+
| sample1              |    1              |    control            |    A               |
+----------------------+-------------------+-----------------------+--------------------+
| sample2              |    1              |    treatment          |    A               |
+----------------------+-------------------+-----------------------+--------------------+
| sample3              |    2              |    treatment          |    A               |
+----------------------+-------------------+-----------------------+--------------------+
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