<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.2.0">
<description>for virus discovery</description>
<requirements></requirements>
<command interpreter="python">
BlastParser_and_hits.py
	--sequences $sequences
	--blast $blast
	--tabularOutput $tabularOutput
	--fastaOutput $fastaOutput
	--flanking $flanking
	--mode $mode
	## Additional parameters.
    #if $additional_filters.use_filters == "yes":
        --filter_relativeCov $additional_filters.filter_relativeCov
        --filter_maxScore $additional_filters.filter_maxScore
        --filter_meanScore $additional_filters.filter_meanScore
    #end if

</command>
<inputs>
	<param name="sequences" type="data" format="fasta"  label="fasta sequences that have been blasted" />
	<param name="blast" type="data" format="tabular" label="The blast output you wish to parse" />
	<param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
	<param name="mode" type="select" label="Verbose or short reporting mode" help="display or not the oases contigs">
	    <option value="verbose" default="true">verbose</option>
	    <option value="short">do not report oases contigs</option>
	</param>
    <conditional name="additional_filters">
            <param name="use_filters" type="select" label="Use Additional Filters?">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no">
            </when>
            <when value="yes">            
                <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
                <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
                <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
            </when>
    </conditional>
</inputs>
<outputs>
	<data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
	<data name="fastaOutput" format="fasta" label="hits"/>
</outputs>

  <tests>
    <test>
        <param ftype="fasta" name="sequences" value="input.fa" />
        <param ftype="tabular" name="blast" value="blast.tab" />
        <param name="flanking" value="5" />
        <param name="use_filters" value="no" />
        <param name="mode" value="verbose" />
        <output name="tabularOutput" ftype="tabular" file="output.tab" />
        <output name="fastaOutput" ftype="fasta" file="output.fa" />
    </test>
  </tests>

<help>

**What it does**

Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly

</help>
</tool>