--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgttable.xml	Wed Nov 27 14:44:13 2013 -0500
@@ -0,0 +1,71 @@
+<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>