<tool id="T2C" name="Get the distribution of the different substitutions">
  <description></description>

  <command interpreter="python">
	/home/galaxy/tools/CTK/T2C.py $input $output_T2Cfiltered $output_substitutions $output_frequencies
  </command>

  <inputs>
        <param name="input" type="data" format="tabular" label="Input unique mutation file of PAR-CLIP 4SU in tabular format"/>
  </inputs>
  
  <outputs>
        <data name="output_T2Cfiltered" format="tabular" label="Tag_uniq_T2C file on ${on_string}" />
        <data name="output_substitutions" format="tabular" label="Tag_uniq_sub file on ${on_string}" />
        <data name="output_frequencies" format="tabular" label="Tag_uniq_freq file on ${on_string}" />
  </outputs>
  <help>

.. class:: infomark

**What this tool does**

It may be useful to get the distribution of the different substitutions that are prevalent. The reason for this is because PAR-CLIP 4SU is known for inducing substitutions (more so than deletions and insertions), specifically by inducing a T to C transition on the forward strand (same as A to G on negative strand).
There are three output files, one of which will be used in the CIMS analysis moving forward.

-----

**Output**

(1) T2Cfiltered file = filtered to only contain T to C substitutions, which we will use in CIMS analysis downstream 

(2) substitutions file = filtered to only contain ALL substitutions (as opposed to all mutations) 

(3) frequencies file = contains a summary of the frequency of all substitutions

Confirm that most of the substitutions are in fact T to C by looking at the frequency column in the frequencies file. 

  </help>
</tool>