<tool id="create_ribosome_profiles" name="Create Ribosome Profiles" version="1.1">
    <description>Produce a sorted bed file of A-Site profiles of RPFs.</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} $refGenomeSource.genomeSource
            #if $refGenomeSource.genomeSource == "builtin":
                none ${refGenomeSource.input1_builtin.fields.path} ${input4} ${output1}
            #else:
                ${refGenomeSource.input1_file} none ${input4} ${output1}
            #end if
    </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"/>
        <conditional name="refGenomeSource">
            <param name="genomeSource" type="select" label="Will you select a reference from your history or use a built-in FASTA?">
                <option value="builtin">Use a built-in FASTA</option>
                <option value="history">Use one from the history</option>
            </param>
            <when value="builtin">
                <param name="input1_builtin" type="select" format="fasta" label="Select a reference" help="if your reference of interest is not listed - contact RiboGalaxy team">
                    <options from_data_table="builtin_fastas">
                        <filter type="sort_by" column="2" />
                        <validator type="no_options" message="No built-ins are available" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="input1_file" type="data" format="fasta" label="FASTA File" />
            </when>
        </conditional>
        <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="bed"/>
    </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="bed" 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>