<tool id="bctools_extract_alignment_ends" name="Extract alignment ends" version="@VERSION@">
    <description>from SAM or BAM</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        extract_aln_ends.py
        '$alignments'
        > '$alignment_ends'
    ]]></command>
    <inputs>
        <param name="alignments" type="data" format="sam,bam" label="Alignments in SAM or BAM format"/>
    </inputs>
    <outputs>
        <data name="alignment_ends" format="bed"/>
    </outputs>
    <tests>
        <test>
            <param name="alignments" value="twomates.sam"/>
            <output name="alignment_ends" file="tworeads_aln_ends.bed"/>
        </test>
    </tests>
    <help><![CDATA[

bctools - Extract alignment ends from from SAM or BAM alignments
================================================================

The resulting BED file contains the outer coordinates of the alignments. The BED
name field is set to the read id and the score field is set to the edit distance
of the alignment. The crosslinked nucleotide is one nt upstream of the 5'-end of
the BED entries.

This tool only reports results for alignments that are properly aligned in FR
("forward-reverse") direction.

Input:
------

* BAM file containing alignments (paired-end sequencing)

Output:
-------

* BED file containing outer coordinates (sorted by read id)

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