<tool id="fromToolshed_Fix_Excel_Mishaps" name="Recover gene symbols" version="0.0.1">
  <description>from dates (e.g. after Excel conversion)</description>
  <command interpreter="perl">
	   genes_not_dates_toolshed.pl --expfile $inFile --cols $marches.date_cols --species $species --resultsfile $outputFile --log $log
	#if $marches.secondary=="yes2":
		--lookup $marches.lookup_col
	#end if
  </command> 
  <inputs>
	<param name="inFile" type="data" checked="yes" format="tabular" label="File with bad gene symbols" />
	<conditional name="marches">
		<param name="secondary" type="select" label="Data to fix includes 1-Mar/MAR or 2-Mar/MAR?" help="Run a Join against these entered as a free-text file to find out quickly.">
			<option value="no2" selected="true">No</option>
			<option value="yes2">Yes</option>
		</param>
		<when value="no2">	
			<param name="date_cols" label="Columns with bad gene symbols to convert" type="data_column" multiple="true" data_ref="inFile" />
		</when>
		<when value="yes2">
			<param name="date_cols" label="Column with bad gene symbols to convert" type="data_column" multiple="false" data_ref="inFile" />
			<param name="lookup_col" label="Column with 2nd gene identifier" type="data_column" multiple="false" data_ref="inFile" help="REQUIRED if 1-Mar or 2-Mar need to be fixed"/>
		</when>
	</conditional>
       	<param name="species" type="select" label="Select species" help="This is necessary for capitalization">
                <option value="human" selected="true">Human</option>
                <option value="mouse">Mouse</option>
        </param>
  </inputs>
  <outputs>
    	<data format="tabular" name="outputFile" label="data_recovered_genesymbols"/>
	<data format="txt" name="log" label="match_info"/>
  </outputs>
  <tests>
    <test>
	<param name="inFile" value="Fix_Excel_Mishaps_in1.tab" ftype="tabular"/>
	<param name="secondary" value="yes2"/>
	<param name="date_cols" value="1"/>
	<param name="lookup_col" value="2"/>
	<output name="outputFile" file="Fix_Excel_Mishaps_data_recovered_genesymbols1.tab"/>
	<output name="log" file="Fix_Excel_Mishaps_match_info1.txt"/>
    </test>
  </tests>
  
  <help>

**What this tool does:**
When Excel sees a gene symbol like SEPT9, it thinks to itself 'that must be a date' and automatically converts it to the date 9-Sep, and one can't ever get the gene symbol back. As an 'after-the-fact' remedy, this tool converts dates like 9-Sept, 3-March, etc, in the chosen column(s) back to the gene symbols SEPT9 and MARCH3, etc. (respectively).


**Note that Excel converts both Marc1/March1 and Marc2/March2 and the human homologs to 1-Mar and 2-Mar, respectively.**
Therefore, without a second identifier, there is no way to tell whether the corresponding gene symbol should be Marc1/2 or March1/2. Appropriate identifiers are NCBI or Ensembl IDs.


</help>


</tool>