<tool id="bctools_extract_crosslinked_nucleotides" name="Get crosslinked nucleotides" version="@VERSION+galaxy1">
    <description>from full alignments</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        coords2clnt.py
        $threeprime 
        '$alignment_coordinates'
        > '$crosslinking_coordinates'
    ]]></command>
    <inputs>
        <param name="alignment_coordinates" type="data" format="bed" label="Alignments in BED format"/>
        <param argument="--threeprime" type="boolean" truevalue="--threeprime" falsevalue="" checked="false"
            label="Set position one nt downstream of 3'-end as crosslinked nucleotide"
            help="Set position one nt downstream of 3'-end as crosslinked nucleotide. By default the crosslink site will be assumed to be one nt upstream of the 5'-end of the read."/>
    </inputs>
    <outputs>
        <data name="crosslinking_coordinates" format="bed"/>
    </outputs>
    <tests>
        <test>
            <param name="alignment_coordinates" value="merged_pcr_dupes.bed"/>
            <output name="crosslinking_coordinates" file="merged_pcr_dupes_clnts.bed"/>
        </test>
    </tests>
    <help><![CDATA[

bctools - Get crosslinked nucleotides from full alignments
==========================================================

Given coordinates of aligned reads in BED format, calculate positions of the
crosslinked nucleotides. Crosslinked nts are assumed to be one nt upstream of
the 5'-end of the read.

Input
-----

* six column BED file containing coordinates of aligned reads

Output
------

* six column BED file containing coordinates of crosslinking events

    ]]></help>
    <expand macro="citations"/>
</tool>