annotate symmetric_plot.xml @ 0:0cac08094b86 draft

"planemo upload for repository https://github.com/QFAB-Bioinformatics/metaDEGalaxy/tree/master/symmetric_plot commit a68579d7bdde7420b8f04346d3b6e361588acf50"

<tool id="symmetricPlot" name="Symmetric Plot" version="1.0.1" hidden="false" force_history_refresh="True">>
  <description>Symmetric Plot</description>
  <requirements>
          <requirement type="package" version="3.4.1">r-base</requirement>
          <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
		  <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
		  <requirement type="package" version="1.20.0">r-getopt</requirement>
		  <requirement type="package" version="0.6.3">r-tidyr</requirement>
		  <requirement type="package" version="9.18">ghostscript</requirement>
<tool id="symmetricPlot2" name="Symmetric Plot" version="1.0.1" hidden="false" force_history_refresh="True">>
  <description>Symmetric Plot</description>
  <requirements>
	  <requirement type="package" version="3.4.1">r-base</requirement>
          <requirement type="package" version="1.22.3">bioconductor-phyloseq</requirement>
	  <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement>
          <requirement type="package" version="1.20.0">r-getopt</requirement>
	  <requirement type="package" version="0.6.3">r-tidyr</requirement>
          <requirement type="package" version="9.18">ghostscript</requirement>
  </requirements>
  <version_command><![CDATA[
	   echo $(R --version | grep version | grep -v GNU)", phyloseq version" $(R --vanilla --slave -e "library(phyloseq); cat(sessionInfo()\$otherPkgs\$phyloseq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
   ]]></version_command>
  <command detect_errors="exit_code"><![CDATA[
	  Rscript '${__tool_directory__}/symmetric_plot.r' 
	  	--input.data='$input_table' 
		--meta.data='$meta_table' 
		--obs.data='$obs_table' 
		--taxrank='$taxonomy_rank' 
		--record='$nTop' 
		--norm="${norm_bool}" 
		--n.column="${selectedCol}" 
		--g.group="${group}" 
		--outdir="$htmlfile.files_path" 
		--htmlfile='$htmlfile' 
  ]]></command>
 
  <inputs>
    <param format="tabular" name="input_table" type="data" label="Count table file"/>
    <param format="tabular" name="meta_table" type="data" label="Metadata file"/>
    <param format="tabular" name="obs_table" type="data" label="OTU Taxonomy file"/>

    <param name="nTop" type="select" display="radio" label="Select number of records to display">
      <option value="20" selected="true">20</option>
      <option value="30">30</option>
      <option value="40">40</option>
      <option value="50">50</option>
      <option value="100">100</option>
    </param>

    <param name="taxonomy_rank" type="select" display="radio" label="Select a taxonomy rank">
      <option value="Kingdom" selected="true">Kingdom</option>
      <option value="Phylum">Phylum</option>
      <option value="Class">Class</option>
      <option value="Order">Order</option>
      <option value="Family">Family</option>
      <option value="Genus">Genus</option>
      <option value="Species">Species</option>
    </param>


    <param name="norm_bool" type="boolean" truevalue="true" falsevalue="false" checked="false" label="is the data normalised?"/> 
    <param name="selectedCol" type="data_column" data_ref="meta_table" use_header_names="TRUE" label="Variable to compare"/>
    <param name="group" type="text" label="Fill in two comparable group separated by comma"/>

  </inputs>
 
  <outputs>
    <data format="html" name="htmlfile" label="${tool.name} SymmetricPlot.html"/>   
  </outputs>

  <tests>
  	<test>
		<param name="input_table" value="count.txt"/>
		<param name="meta_table" value="metadata.txt"/>
		<param name="obs_table" value="observation.txt"/>
		<param name="nTop" value="30"/>
		<param name="taxonomy_rank" value="Phylum"/>
		<param name="selectedCol" value="3"/>
		<param name="group" value="Early,Late"/>
		<output name="htmlfile" ftype="html" file="SymmetricPlot.html"/></test>
   </tests>
  <help>
.. class:: infomark

**TIP:** The input data should be in tabular format.

.. class:: infomark

**TIP:** The first column should contain OTU ID.

.. class:: infomark

**TIP:** This program takes in two files:1)raw count/normalised table, 2) a metadata file
   
.. class:: infomark
  
**What it does**
 
 This program uses an R package called DESeq2_ and ggplot2_ to create a symmetric bar plot.

.. _DESeq2 : https://bioconductor.org/packages/release/bioc/html/DESeq2.html
.. _ggplot2: https://ggplot2.tidyverse.org/

=======
 This program uses an R package called DESeq2 and ggplot2 to create a symmetric bar plot.
  
-----

**Syntax**

This tool creates a symmetric plot based on input table. The input table,if it is a raw count table, will be normalised by DESeq "counts" function with flag "normalised=T".
   
- **A normalised dataset** - set to "Yes" only if the input table is a normalised dataset
- **Group of choice** - The group of choice will appear in the title of the plot(e.g., Tissue, protein and etc).
- **Select a group** - This is a list of group to use in comparison(e.g., Tissue A vs Tissue B). This should be the same as "Group of choice".
- **Select only two groups to compare** - select only two groups of interest for comparison.

-----

=========
Resources
=========

=======
**Wrapper Author**

QFAB Bioinformatics ([e-mail])

  </help>
  <citations>
  	<citation type="doi">10.18129/B9.bioc.DESeq2</citation>
	<citation type="doi">10.1007/978-3-319-24277-4</citation>
  </citations>
=======
</tool>