<tool id="virannot_blast2tsv" name="virAnnot Blast2tsv" version="1.0.1+galaxy0" profile="21.05">
    <description>convert XML blast results to tabular file with taxonomic informations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements" />
    <required_files>
        <include path="blast2tsv.py" />
    </required_files>
    <command detect_errors="aggressive"><![CDATA[
    python '$__tool_directory__/blast2tsv.py' 
        -x '$blast_xml' 
        -c '$contigs' 
        -a '$blast_type' 
        -me '$max_evalue'
        #if $read_nb
            -rn '$read_nb'
        #end if
    ]]></command>
    <inputs>
        <param type="data" name="blast_xml" format="blastxml" label="Blast results file" />
        <param type="data" name="contigs" format="fasta" label="Contigs" />
        <param type="select" name="blast_type" label="Type of blast">
            <option value="BLASTX">BLASTX</option>
            <option value="BLASTP">BLASTP</option>
            <option value="TBLASTX" selected="true">TBLASTX</option>
            <option value="BLASTN">BLASTN</option>
            <option value="DIAMOND">DIAMOND</option>
        </param>
        <param type="select" name="max_evalue" label="Maximum evalue">
            <option value="0">0</option>
            <option value="0.1">0.1</option>
            <option value="0.01">0.01</option>
            <option value="0.001" selected="true">0.001</option>
            <option value="0.0001">0.0001</option>
        </param>
        <param type="data" name="read_nb" format="tabular" label="Read number file" optional="true" />
    </inputs>
    <outputs>
        <data name="out_annotation" format="tabular" from_work_dir="blast2tsv/blast2tsv_output.tab" label="${tool.name} on ${on_string} : annotation" />
        <data name="out_reads" format="tabular" from_work_dir="blast2tsv/blast2tsv_reads.txt" label="${tool.name} on ${on_string} : output reads" />
        <data name="out_contigs" format="tabular" from_work_dir="blast2tsv/blast2tsv_contigs.txt" label="${tool.name} on ${on_string} : output contigs" />
    </outputs>
    <tests>
        <test>
            <param name="blast_xml" value="blast2tsv_input.xml"/>
            <param name="contigs" value="blast2tsv_contigs.fa"/>
            <param name="blast_type" value="TBLASTX"/>
            <param name="max_evalue" value="0.001"/>
            <output name="out_annotation" file="blast2tsv_output.tab">
                <assert_contents>
                    <has_n_columns n="16" />
                    <has_n_lines n="13" />
                    <has_text text="NODE_13_length_295_cov_0.945833" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="blast_xml" value="blast2tsv_input.xml"/>
            <param name="contigs" value="blast2tsv_contigs.fa"/>
            <param name="blast_type" value="TBLASTX"/>
            <param name="max_evalue" value="0.001"/>
            <param name="read_nb" value="blast2tsv_read_nb.tab"/>
            <output name="out_annotation" file="blast2tsv_output_with_rn.tab">
                <assert_contents>
                    <has_text text="pfam13603" />
                    <has_n_lines n="13" />
                </assert_contents>
            </output>
            <output name="out_annotation" file="blast2tsv_reads_with_rn.txt">
                <assert_contents>
                    <has_text text="Desulfovibrio" />
                    <has_n_lines n="13" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        
This module takes as input blast file from blast annotation and fasta contig file.
Set the right blast type or else the query overlap and hit overlap values will be wrong.
For TBLASTX type, the standard maximum evalue is 0.001.

    ]]></help>
    <expand macro="citations"/><!--rajouter ete3-->
</tool>