<tool id="snp_caller" name="Snip Finder" version="0.1.0">
    <description>Identifies snips for both single-end and paired-end data</description>
    <requirements>
        <requirement type="package" version="0.1">snp_caller</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
	snp
	    -amr_fp $reference
	    #if $sam_type.mode == "single_end"
	    -samse $sam_type.samse_input
	    $sam_type.best
	    #else
	    -sampe $sam_type.sampe_input
	    $sam_type.best
	    #end if
	    -out_fp $result
    ]]></command>
    <inputs>
	<param type="data" name="reference" format="fasta" label="Reference sequence"/>
	<conditional name="sam_type">
	    <param name="mode" type="select" label="SAM file type">
	        <option value="single_end"></option>
		<option value="paired_end"></option>
	    </param>
	    <when value="single_end">
	        <param type="data" name="samse_input" format="sam" label="Single-end SAM file"/>
		<param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/>
	    </when>
	    <when value="paired_end">
		<param type="data" name="sampe_input" format="sam" label="Paired-end SAM file"/>
		<param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/>
	    </when>
	</conditional>
    </inputs>
    <outputs>
	<data name="result" format="tabular" />
    </outputs>
    <tests>
	<test>
	    <param name="mode" value="single_end"/>
            <param name="reference" value="ref.fa"/>
            <param name="samse_input" value="samse.sam"/>
            <output name="result" file="samse_result" ftype="tabular"/>
        </test>
	<test>
	    <param name="mode" value="paired_end"/>
	    <param name="reference" value="ref.fa"/>
	    <param name="sampe_input" value="sampe.sam"/>
	    <output name="result" file="sampe_result" ftype="tabular"/>
	</test>
    </tests>
    <help><![CDATA[
This program parses a SAM file and looks for single nucleotide polymorphisms (SNPs). In single-end mode, only alignments with bit four not set are considered. In paired-end mode, only reads that mapped in a proper pair are considered. When filtering on unique alignments, only alignments with the XT:A:U field are considered.

Program: snpfinder

Contact: Chris Dean <cdean11@rams.colostate.edu>

Usage: snp [options]

Options:
    -amr_fp	amr database path
    -samse	single-end sam file path
    -sampe	paired-end sam file path
    -b		filter on unique alignments
    ]]></help>
    <citations>
    </citations>
</tool>