<tool id="gene_fraction" name="Coverage sampler" version="0.1.0">
    <requirements>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
	csa
	    -amr_fp $input1
            -sam_fp $input2
	    -min $min
	    -max $max
	    -skip $skip
	    -t $threshold
	    -samples $samples
	    -out_fp $output1
    ]]></command>
    <inputs>
	<param type="data" name="input1" format="fasta" />
	<param type="data" name="input2" format="sam" />
	<param name="min" type="integer" label="Minimum sample value"
	       value="1" min="1" max="100" help="(-min)" />
	<param name="max" type="integer" label="Maximum sample value"
		value="1" min="1" max="100" help="(-max)" />
	<param name="skip" type="integer" label="Amount of levels to skip"
		value="1" min="1" max="100" help="(-skip)" />
	<param name="threshold" type="integer" label="Gene fraction threshold"
		value="1" min="1" max="100" help="(-t)" />
	<param name="samples" type="integer" label="Amount of samples per level"
		value="1" min="1" max="100" help="(-samples)" />
    </inputs>
    <outputs>
	<data name="output1" format="tabular" />
    </outputs>
    <help><![CDATA[
        
Program: Coverage Sampler 
Contact: Chris Dean <cdean11@rams.colostate.edu

Usage: csa [options]

Options:

    -amr_fp    amr database path
    -sam_fp    sam file path
    -min       starting level
    -max       ending level
    -skip      amount of levels to skip
    -t         gene fraction threshold
    -samples   amount of samples per level
    -d         directory parsing
    -bam       bam file parsing
    -out_fp    output file path


    ]]></help>
</tool>