<tool id="coords2clnt.py" name="Get crosslinked nucleotides" version="0.1.0">
  <description>from full alignments</description>
  <xml name="requirements">
      <requirements>
          <requirement type="package" version="0.6.9">pybedtools</requirement>
      </requirements>
  </xml>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <stdio>
    <exit_code level="fatal" range="1:"/>
  </stdio>
  <version_command>python $__tool_directory__/coords2clnt.py --version</version_command>
  <command interpreter="python"><![CDATA[coords2clnt.py
#if $positional_1 and $positional_1 is not None:
$positional_1
#end if

> $default]]></command>
  <inputs>
    <param area="false" label="Alignments in bed format." name="positional_1" type="data" format="bed"/>
  </inputs>
  <outputs>
    <data hidden="false" name="default" format="bed"/>
  </outputs>
  <tests>
    <test>
      <param name="positional_1" value="merged_pcr_dupes.bed"/>
      <output name="default" file="merged_pcr_dupes_clnts.bed"/>
    </test>
  </tests>
  <help><![CDATA[
Given coordinates of the aligned reads, calculate positions of the crosslinked nucleotides.
Crosslinked nts are assumed to be one nt upstream of the 5'-end of the read.

Input:

* bed6 file containing coordinates of aligned reads
* bed6 file containing coordinates of crosslinking events

Author: Daniel Maticzka
Copyright: 2015
License: Apache
Email: maticzkd@informatik.uni-freiburg.de
Status: Testing
]]></help>
  <expand macro="citations" />
</tool>