<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.4.2">
<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"
        --filter_term_in "$additional_filters.filter_term_in"
        --filter_term_out "$additional_filters.filter_term_out"
    #end if
    --al_sequences "$al_sequences"
    --un_sequences "$un_sequences"
    --dataset_name "$blast.element_identifier"

</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="Extensive or compact  reporting mode" help="display (extensive)  or not (compact) the oases contigs">
	    <option value="verbose" default="true">extensive</option>
	    <option value="short">compact</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=""/>
                <param name="filter_term_in" type="text" value="" label="filter the subject list with a keyword" help=""/>
                <param name="filter_term_out" type="text" value="" label="filter the subject list excluding a keyword" help=""/>
            </when>
    </conditional>
</inputs>
<outputs>
	<data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
	<data name="fastaOutput" format="fasta" label="hits"/>
	<data name="al_sequences" format="fasta" label="Blast aligned sequences"/>
	<data name="un_sequences" format="fasta" label="Blast unaligned sequences"/>
</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" />
        <output name="al_sequences" ftype="fasta" file="al_sequences.fa" />
        <output name="un_sequences" ftype="fasta" file="un_sequences.fa" />
    </test>
  </tests>

<help>

**What it does**

Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly. Outputs also the contig sequences which have or not been blast aligned taking into account all indicated cut-offs

</help>
</tool>