<tool id="get_chrom_sizes" name="Get Chromosome Sizes" version="2.2">
    <description>Chromosome sizes are needed for the creation of ribosome profiles. This tool generates a tab delimited chrom.sizes file from an inputted fasta</description>
    <command>
        python $__tool_directory__/calculating_chrom.sizes.py ${refGenomeSource.genomeSource} 
            #if $refGenomeSource.genomeSource == "history":
                ${refGenomeSource.genomeSource.input1_file}
            #else:
                ${refGenomeSource.genomeSource.input1_builtin} 
            #end if
            ${input2} ${output1}
    </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" 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="select" label="Chromosome Column Prefix (eg. chr)">
            <option value="chr">'chr' (required for upload to GWIPS-Viz)</option>
            <option value="none" selected='true'>None - do not add a prefix</option>
            <option value="manual">Specify you own</option> 
        </param> 

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