<?xml version="1.0" encoding="UTF-8"?>
<tool id="bam2roi" name="Bam2roi">
    <command>bam2roi
    $bam2roi_verbose
    $bam2roi_very_verbose
    --input-file "$bam2roi_input_file"
    --output-file "$bam2roi_output_file"
    $bam2roi_strand_specific
    $bam2roi_ignore_pairing
    $bam2roi_link_over_skipped
    #if $bam2roi_input_file
        --input-file-file-ext ${bam2roi_input_file.ext}
    #end if
    #if $bam2roi_output_file
        --output-file-file-ext ${bam2roi_output_file.ext}
    #end if</command>
    <description>Create ROI from BAM file.</description>
    <inputs>
        <param falsevalue="" truevalue="--verbose" type="boolean" name="bam2roi_verbose" label="Verbose mode." />
        <param falsevalue="" truevalue="--very-verbose" type="boolean" name="bam2roi_very_verbose" label="Very verbose mode." />
        <param falsevalue="" truevalue="--link-over-skipped" type="boolean" name="bam2roi_link_over_skipped" label="Link over skipped bases in the read alignment." />
        <param falsevalue="" truevalue="--ignore-pairing" type="boolean" name="bam2roi_ignore_pairing" label="Ignore paired information.  Also see Section ROI Creation Details." />
        <param label="SAM/BAM formatted file.  Must be sorted by coordinate." type="data" name="bam2roi_input_file" format="sam,bam" />
        <param falsevalue="" truevalue="--strand-specific" type="boolean" name="bam2roi_strand_specific" label="Calculate strand-specific ROIs (see section Strand Specificness below." />
    </inputs>
    <outputs>
        <data label="Output file with regions of interest." name="bam2roi_output_file" format="roi" />
    </outputs>
    <stdio>
        <exit_code range="1:" level="fatal" />
        <exit_code range=":-1" level="fatal" />
    </stdio>
</tool>
