<tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.0">
    <description>Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.</description>
    <requirements>
        <requirement type="package" version="1.79">biopython</requirement>
        <requirement type="package" version="0.19.0">pysam</requirement>
    </requirements>
    <command>python $__tool_directory__/bam_to_ribosome_profile.py ${input1} ${input2} ${input3} ${input4}</command>
    <inputs>
        <param name="input1" type="data" format="bam" label="BAM file to process"/>
        <param name="input2" type="integer" value="15" label="Offset to use" help="Use 15 for elongating ribosomes, 12 for initiating and 0 form RNA-seq reads"/>
        <param name="input3" type="data" format="fasta" label="FASTA file to which the reads were aligned"/>
        <param name="input4" type="select" label="Approach" help ="Use Offset for RNase and Weight for MNase">
            <option value="offset" selected="true">Use offset approach</option>
            <option value="weight">Use weight centered approach</option>
        </param>
    </inputs>
    <outputs>
       <data name="output1" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="test.bam.sorted"/>
            <param name="input2" value="15"/>
            <param name="input3" value="sacCer3_transcripts.fasta"/>
            <param name="input4" value="offset"/>
            <output name="output1" file="test.bam.sorted.bed.sorted " ftype="tabular" lines_diff="4" />
        </test>
    </tests>
    <help>
    **What it does**

    Produce a sorted bed file from a sorted BAM file with the option of introducing an offset to the A-Site of a ribosome protected fragment.

    </help>
    <citations/>
</tool>