merge_three_replicates.xml

<tool id="merge_three_replicates" name="Merge three biological replicates"  version='17.09'>
  <description></description>
  <command><![CDATA[
    /home/miniconda2/bin/bedtools sort -i ${peak1} > ${peak1}_sort.bed &&
    /home/miniconda2/bin/bedtools sort -i ${peak2} > ${peak2}_sort.bed &&
	/home/miniconda2/bin/bedtools sort -i ${peak2} > ${peak2}_sort.bed &&
	/home/miniconda2/bin/bedtools intersect -a ${peak1}_sort.bed -b ${peak2}_sort.bed | cut -f1-3 | sort | uniq > ${peak1}_${peak2}.bed &&
	/home/miniconda2/bin/bedtools intersect -a {peak1}_${peak2}.bed -b ${peak3}_sort.bed | cut -f1-3 | sort | uniq > ${outBed}
  ]]></command>

  <inputs>
  	<param name="peak1" type="data" format="tsv,encodepeak,bed,txt"  multiple="false" label="Peak regions for biological replicate 1" help=""/>
    <param name="peak2" type="data" format="tsv,encodepeak,bed,txt"  multiple="false" label="Peak regions for biological replicate 2" help=""/>
	<param name="peak3" type="data" format="tsv,encodepeak,bed,txt"  multiple="false" label="Peak regions for biological replicate 3" help=""/>
  </inputs>

  <stdio>
	<exit_code range="1:"  level="fatal" description="Error Running combine collection to a file" />
  </stdio>
  <outputs> 
	<data name="outBed" format="txt" label= "intersect.bed">
	</data>
  </outputs>
  <help>

.. class:: infomark

**What it does**

This function is designed to obtain consistent RNA modifications among three biological replicates by using bedtools.

.. class:: infomark

**Inputs**

- **Peak regions for biological replicate 1**
- **Peak regions for biological replicate 2**
- **Peak regions for biological replicate 3**

**Outputs**

- **Consistent peak regions among three biological replicates**

</help>
</tool>