<tool name="GIANT-Factor file generator" id="giant_factor_generator" version="0.1.2">
  <description>Generate factor file used by other GIANT tools</description>
  <requirements>
  </requirements>
  <code file="../../src/General_functions.py"/>
  <stdio>
    <regex match="Execution halted"
           source="both"
           level="fatal"
           description="Execution halted, please contact tool developer or administrators." />
    <regex match="Error in"
           source="both"
           level="fatal"
           description="An error occured during R execution, please contact tool developer." />
    <exit_code range="1:9" level="fatal" description="Error during factor file generation, see log file for more information." />
  </stdio>
  <command>	<![CDATA[

  #import imp
  #set $general_functions=$imp.load_source('General_functions', $__tool_directory__+'/../../src/General_functions.py')

  #set $ret_code=$general_functions.generateFactorFile($inputCondition['inputData'],$factorsSection['factorList'],$outputData.file_name,$log.file_name)

  if [ $ret_code != 0 ]; then
    printf "[ERROR]Error during factor file generation\n" >> $log;
    exit $ret_code;
  fi;

  printf "[INFO]End of tool script" >> $log; 
	]]>
  </command>
  <inputs>
  <param type="text" name="title" value="ConditionsGenerator_toPersonalize" label="Title for output"/>

  <conditional name="inputCondition">
      <param name="selection" type="select" label="Input data type for sample names" force_select="true">
        <option value="normalizedData">Expression tabular file</option>
        <option value="CELcollection">.CEL files</option>
      </param>
      <when value="normalizedData">
        <param type="data" name="inputData" format="tabular" label="Select file" optional="false" multiple="false"/>
      </when>
      <when value="CELcollection">
        <param type="data" name="inputData" format="cel" label="Select files" optional="false" multiple="true">
        <validator type="empty_dataset" message="At least one data file should be selected"></validator>
        </param>
      </when>
  </conditional>

  <section name="factorsSection" title="Factor definition" expanded="True">
     <repeat name="factorList" title="Factor">
        <param type="text" name="factorName" value="" label="Factor name"/>
        <repeat name="valueList" title="Value">
          <param type="text" name="valueName" value="" label="Value name"/>
          <param name="valueConditions" type="select" optional="false" multiple="true" label="Select sample sharing this value"
            refresh_on_change="true"  dynamic_options="get_condition_file_names(inputCondition['inputData'])">
          </param>
        </repeat>
    </repeat>
  </section>
	
  </inputs>

  <outputs>
    <data format="tabular" name="outputData" label="${title}_conditionsFile"/>

    <data format="txt" name="log" label="${title}_Log" />
  </outputs>
  
 <tests>
  <test maxseconds="3600">
    <param name="wfile" value="wiggle.wig" />
    <param name="bfile" value="bedfile.bed" />
    <param name="span" value="3000" />
    <param name="pfres" value="50" />
    <param name="lowersize" value="1000" />
    <param name="middlesize" value="2000" />
    <param name="uppersize" value="3000" />
    <param name="lowerbisize" value="2500" />
    <param name="upperbisize" value="5000" />
    <param name="reldist" value="3000" />
    <param name="genome" value="hg18" />
    <param name="imagetype" value="PDF" />
    <param name="enable" value="no" />
    <output name="outputData" file="ceas_1/ceas_1.pdf" />
  </test>
</tests> 
  <help>
<![CDATA[
**What it does ?**

This tool generates factor information file used by other tools of GIANT tool suite.

-----

**Parameters**

\- **Title** to personalize output file names (please avoid special characters and spaces).

\- **Input Data** used only to extract sample names

- **Expression tabular file** with samples as columns and genes as rows (only the header row will be used to extract sample names).

    ::

        Conditions  157_(HuGene-2_0-st).CEL 156_(HuGene-2_0-st).CEL  155_(HuGene-2_0-st).CEL    154_(HuGene-2_0-st).CEL                        
        DDX11L2     4.500872                4.429759                 4.780281                   4.996189             
        MIR1302-2   3.415065                3.520472                 3.471503                   3.567988           
        OR4F5       3.737956                3.011586                 3.424494                   3.497545
        VWA1        5.189621                5.129595                 4.806793                   5.227014

OR

- **.CEL files** of your study (you should select multiple .CEL files or unique collection file).

\- **Factor definition**

- **Factor name** to discriminate between samples as 'Treatments', 'Year', 'Strain' (please avoid special characters)

- **Value name** of different states for the current factor as 'KO' or 'WT' for 'Strain' factor (please avoid special characters)

- **Select sample** to assign to current value

-----

**Outputs**

- **Factor information tabular file**  with factors as columns and samples as rows (header row contains factor names and first column sample names).

    ::

        Conditions                Sex   Treatment Reaction
        138_(HuGene-2_0-st).CEL   1     TreatA    Pos
        148_(HuGene-2_0-st).CEL   0     NoTreat   Pos
        139_(HuGene-2_0-st).CEL   0     TreatB    Neg
        149_(HuGene-2_0-st).CEL   0     NoTreat   Neg

- **LOG file** for job log. If you see errors, please attached this in the bug report

]]>  </help>

 <citations>
 </citations>

</tool>