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<tool id="CITS" name="CITS analysis">
  <description></description>
  
  <command interpreter="perl">
	/home/galaxy/tools/CTK/CITS.pl -v $bigFile -p $pvalue $multitest --gap $gap $uniqTagBed $uniqMutationTypeBed $output
  </command>

  <inputs>
        <param type="data" format="bed" name="uniqTagBed" label="Input file in BED format of unique tags"/>
        <param type="data" format="bed" name="uniqMutationTypeBed" label="Input file in BED format of deletions, insertions, or substitutions corresponding to the tags above" />
    
        <param name="bigFile" type="boolean" truevalue="-big" falsevalue="" checked="yes" label="This is a big file (over 6M lines)" />
        <param name="pvalue" type="float" value="0.001" label="Threshold of p-value of CITS" />
	<param name="multitest" type="boolean" truevalue="--multi-test" falsevalue="" checked="yes" label="Do Bonferroni multiple test correction" />
        <param name="gap" type="integer" value="25" label="Minimum gaps allowed between peaks (no merge cluster peaks if less than 0)" />
  </inputs>

  <outputs>
        <data name="output" format="bed" label="CITS analysis on ${on_string}"/>
  </outputs>

  <help>

.. class:: warningmark

Only certain variations of the CLIP protocol allow you to perform CITS analysis (e.g. iCLIP, BrdU CLIP, etc).

-----

.. class:: infomark

**What this tool does**

Cross-linking induced trunction site (CITS) analysis

Similar to CIMS analysis, This tool identifies clustered truncation sites and assigns statistical significance of the clustering based on a permutation based procedure. 

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Reference:

Weyn-Vanhentenryck,S.,M.*, Mele,A.*, Yan,Q.*, Sun,S., Farny,N., Zhang,Z., Xue,C., Herre,M., Silver,P.A., Zhang,M.Q., Krainer,A.R., Darnell,R.B. †, Zhang,C. † 2014. HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep. 10.1016/j.celrep.2014.02.005. 

   </help>
</tool>