<?xml version="1.0"?>

<tool name="Calculate highest expressed TFs" id="highestTF">
  <description>
    e.g. expression index > x, ranked by expression level
  </description>
  <code file="exptf_code.py"/>
  <command interpreter="python">
  exptf.py '$expression_index_file' '$i' '$cutoff' '$filterSource' '$coactivator' '$corepressor' '$tf' '$tr' '$log'
  </command>

  <inputs>
    <page>
      <param name="title" type="text" label="Enter a label for the output file" value="Highest TFs"/>
      <param name="expression_index_file" type="data" format="txt" label="Expression index file (Required)" 
	     optional="false" size="120" help="Choose an expression index file from your current history"/>
    </page>
    <page>
      <param name="i" type="select" label="Sample"
	     dynamic_options="getSampleNames(expression_index_file)"
	     help="Please choose a sample from the expression index file to find highest expressed TFs">
      </param>
      <param name="cutoff" type="float" label="Expression value cutoff" value="10" required="true"
	     help="Expression value cutoff point above which genes will be selected"/>
      <param name="filterSource" type="select" label="Use GO filters">
	<option value="Nil">Not using</option>
	<option value="Human">Human</option>
	<option value="Mouse">Mouse</option>
	<option value="Fly">Fly</option>
	<option value="CElegans">C elegans</option>
      </param>
      <param name="coactivator" type="boolean" truevalue="T" falsevalue="F" label="Filtered by transcription coactivator activity GO:0003713"/>
      <param name="corepressor" type="boolean" truevalue="T" falsevalue="F" label="Filtered by transcription corepressor activity GO:0003714"/>
      <param name="tf" type="boolean" truevalue="T" falsevalue="F" label="Filtered by transcription factor activity GO:0003700"/>
      <param name="tr" type="boolean" truevalue="T" falsevalue="F" label="Filtered by transcription regulator activity GO:0030528"/>
    </page>
  </inputs>

  <outputs>
    <data format='txt' name="log" label="${title}"/>
  </outputs>
  <help>
  
**Syntax**

- **Title:**  Label for the output file
- **Expression index file:** Select a Normalized Expression Index (.txt)  file from your history
- **Sample:** Select a  sample name from the expression index file to find highest expressed TFs
- **Expression value cutoff:** Expression value cutoff point above which genes will be selected
- **Filtered by transcription:** Allow you to select 4 different TFs GO terms 

-----

**Summary**

Provided a Expression Index (.txt) file as input, this tool allows you to calculate highest expressed Transcription Factors, the selection is done based in a  expression index cutoff value  x  and  further filtering can be done to restrict the resulting list to transcription regulator activity (GO:0030528),  transcription factor activity (GO:0003700), transcription co-repressor activity (GO:0003714) or transcription co-activator activity (GO:0003713).

The expected format for the input Expression Index file, contains sample names in the columns and Gene symbols in the rows as follow:

::
    
    Name     Sample1        Sample2        Sample3
    Gene1    Exp.Value11    Exp.Value12    Exp.Value13
    Gene2    Exp.Value21    Exp.Value22    Exp.Value23
    Gene3    Exp.Value31    Exp.Value32    Exp.Value33

You could  either upload such file using the "**Galaxy:Get Data**/Upload File from your computer" tool, or obtain this file as result of the Gene expression index tool. In both cases, you will be able to select the target file from your history.  After the file is selected, you should choose a sample from the expression index file to find highest expressed, specify the Expression value cutoff, and select the transcription factor filter accordingly.  If no filter is selected, all expression values will be reported.
The output will be a text file showing the  list of the highest expressed TFs, with the following columns: Gene, exp_value, Reference, Evidence,  Name(s), Synonyms  and Assigned by


  </help>
</tool>