<tool id="rarefaction_analyzer" name="ResistomeAnalyzer" version="0.1.0">
    <description>A simple tool for creating rarefaction curves for metagenomic sequence data</description>
    <requirements>
	<requirement type="package" version="0.1">rarefactionanalyzer</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
	rarefaction
	  -ref_fp $reference
	  -annot_fp $annotation
	  -sam_fp $sam
	  -min $min
	  -max $max
	  -t $threshold
	  -samples $samples
	  -skip $skip
	  -gene_fp $gene
	  -mech_fp $mech
	  -class_fp $class
	  -group_fp $group
    ]]></command>
    <inputs>
	<param type="data" name="reference" format="fasta" label="Reference sequence" />
	<param type="data" name="sam" format="sam" label="SAM file" />
	<param type="data" name="annotation" format="csv" label="Annotation file" />
	<param name="min" type="integer" label="Starting sample level"
	       value="1" min="1" max="100" help="(-min)" />
	<param name="max" type="integer" label="Ending sample level"
	       value="1" min="1" max="100" help="(-max)" />
	<param name="threshold" type="integer" label="Gene fraction threshold"
	       value="0" min="0" max="100" help="(-t)" />
	<param name="skip" type="integer" label="Amount of sample levels to skip"
	       value="1" min="1" max="100" help="(-skip)" />
	<param name="samples" type="integer" label="Iterations per sample level"
	       value="1" min="1" max="100" help="(-samples)" />
    </inputs>
    <outputs>
	<data name="gene" format="tabular" />
	<data name="mech" format="tabular" />
	<data name="class" format="tabular" />
	<data name="group" format="tabular" />
    </outputs>
    <citations>
    </citations>
</tool>