<?xml version="1.0"?>

<tool name="Draw a histogram/box plot" id="expindxplotId">
  <description>
    of Expression index for a given a list of Genes
  </description>
  <code file="eiplot_code.py"/>
  <command interpreter="python">
  eiplot.py  '$title' '$expression_index_file' '$opMode.sampleName' '$opMode.geneList1' '$opMode.refChoice' '$opMode.geneList2' '$logmeta'
  </command>

  <inputs>
    <page>        
        <param name="title" label="Title to label the new output file" type="text" size="80" value="Expression Index Plot" />
        <param name="expression_index_file" type="data" format="txt" label="Expression index file" 
         optional="false" size="120" help="Choose an expression index file from your current history"/>
    </page>
    <page>
        <conditional name="opMode">

       <param name="opMode" type="select" label="Operation Type">
            <option value="basic" selected="true">Basic</option>
            <option value="advanced">Advanced</option>
        </param>

        <when value="basic">
            <param name="sampleName" type="select" label="Samples from the Expression Index File"
            dynamic_options="getSampleNames(expression_index_file)"
            help="Choose a sample from the expression index file">
            </param>

            <param name="geneList1" type="data" format="txt" label="Select a second gene list to compare"
            optional="false" size="120" help="Choose a gene list file from your current history.Genes must be separated by new line."/>

            <param name="refChoice" type="hidden" value="All"/>
            <param name="geneList2" type="hidden" value=""/>

        </when>
        <when value="advanced">
            <param name="sampleName" type="select" label="Samples from the Expression Index File"
            dynamic_options="getSampleNames(expression_index_file)"
            help="Choose a sample from the expression index file">
            </param>

            <param name="geneList1" type="data" format="txt" label="Select a second gene list to compare"
            optional="false" size="120" help="Choose a gene list file from your current history.Genes must be separated by new line."/>

            <param name="refChoice" type="select" display="radio" label="Select Genes">
            <option value="All">All Genes in the expression index file</option>
            <option value="Partial">Choose a partial gene list file</option>
            </param>

            <param name="geneList2" type="data" format="txt" label="Partial expression index genes"
            optional="true" size="120" help="Choose a partial genes file from your current history. Genes must be separated by new line.  "/>

        </when>

    </conditional>


       
    </page>
  </inputs>

  <outputs>     
    <data format='txt' name="logmeta"/>
  </outputs>
  <help>

**Syntax**

- **Title:**  Label for the output file
- **Expression index file:** Select a Normalized Expression Index (.txt)  file from your history
- **Samples from the Expression Index File:**   Select the sample column that will serve as reference
- **Select a Gene List to compare:**  Choose from your history a gene symbol list to compare
- **Select Genes:** You could select all other genes from the previously selected sample as "gene universe" to compare the expression or
- **Select a second gene list to compare:** If you want to compare 2  gene list among each other, you should select a gene list 2

-----

**Summary**

This tool allows you to visualize (box plot and histograms) the expression index distribution of:

- One gene list when compared with the "gene universe" of all other genes for a particular sample or
- Two gene lists to compare the expression distribution of one list with the other

The output of this tool is a .pdf file containing 3 figures.

- Box plot of the compared Expression Index
- Expression distribution histogram of gene list 1
- Expression distribution histogram of gene list 2 or gene universe

  </help>
</tool>