<tool id="rgttable" name="Read Group Tracking Table" version="1.0">
  <description>Generate FPKM tables from cuffdiff read_group_tracking files.</description>
  <command interpreter="perl"> 
    rgttable.pl
    #if $column.selcol == 'yes':
      -c $column.colnum 
    #end if
    $rgt_in $rgt_out
  </command>
  <inputs>
    <param name="rgt_in" type="data" format="tabular" label="Input file" />
    <conditional name="column">
      <param name="selcol" type="select" label="FPKM column" >
        <option value="no" selected="true">Use column 7 for the value (default for FPKM)</option>
        <option value="yes" >Select the column to use for the value</option>
      </param>
      <when value="no"/>
      <when value="yes">
        <param name="colnum" type="data_column" data_ref="rgt_in" numerical="true" optional="true" label="column" />
      </when>
    </conditional>
    <!--
    <param name="column" type="integer" value="7" label="Data column to keep (default 7)" />
    -->
  </inputs>
  <stdio>
  </stdio>
  <outputs>
    <data name="rgt_out" format="tabular" />
  </outputs>
  <tests>
    <test>
      <param name="rgt_in" ftype="tabular" value="genes.read_group_tracking" />
      <param name="selcol" value="no" />
      <output name="rgt_out" file="genes.rgt.tsv" />
    </test> 
  </tests>
  <help>
This script converts read group tracking files produced by Cuffdiff into a format useful
for importing into other programs. 
The output has a row for each tracking_id, with a column for tracking_id, and additional columns for each unique combination of condition and replicate.  

This works with the isoforms, genes, cds, and tss_groups
read group tracking files generated by cuffdiff.

INPUT
A cuffdiff read_group_tracking file

 ============= =========== =========== =========== ===================== ===================== ========= ================ ======== 
  tracking_id   condition   replicate   raw_frags  internal_scaled_frags external_scaled_frags   FPKM    effective_length  status  
 ============= =========== =========== =========== ===================== ===================== ========= ================ ======== 
  AES           heart               0           1              1.15043               1.15043    18.1912   =                 OK     
  AES           heart               1           1              0.800708              0.800708   18.5033   =                 OK     
  AES           heart               2           4              2.96393               2.96393    68.5644   =                 OK     
  AES           skeletal            0           0              0                     0           0        =                 OK     
  AES           skeletal            1           1              1.05362               1.05362    25.0567   =                 OK     
  AES           skeletal            2           0              0                     0           0        =                 OK     
 ============= =========== =========== =========== ===================== ===================== ========= ================ ======== 

OUTPUT

 ============= ========= ========= ========= ============ ============ ============ 
  tracking_id   heart-0   heart-1   heart-2   skeletal-0   skeletal-1   skeletal-2  
 ============= ========= ========= ========= ============ ============ ============ 
  AES           18.1912   18.5033   68.5644            0      25.0567            0  
 ============= ========= ========= ========= ============ ============ ============ 

  
  
  </help>
</tool>