<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.8.2">
    <description>Generates a TAB Delimited chrom.sizes File from an Inputted FASTA</description>
    <requirement type="package" version="1.13">samtools</requirement>

    <command>

        #if $refGenomeSource.genomeSource == "builtin":
            samtools index ${refGenomeSource.input1_builtin.fields.path}
            cut -f 1,2 ${refGenomeSource.input1_builtin.fields.path}.fai > $output1
        #else:
            samtools index ${refGenomeSource.input1_file}
            cut -f 1,2 ${refGenomeSource.input1_file}.fai > $output1
        #end if

    </command>
    <inputs>
        <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="input2" type="text" label="Chromosome Column Prefix (add chr if absent from FASTA file for GWIPS upload)" />

    </inputs>
    <outputs>
       <data name="output1" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="test.fasta" ftype="fasta" />
            <param name="input2" value="chr"/>
            <output name="output1" file="test.fasta.sizes" ftype="tabular" lines_diff="4" />
        </test>
    </tests>
    <help>
**What it does**

Creates a chromosome sizes file from a fasta file. This is needed for creating ribosome profiles. 

Some commonly used genomes are provided to save on storage.
    </help>
    <citations/>
</tool>