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<tool id="edu.tamu.cpt.blastn_to_gff3" name="BlastN Results to GFF3" version="19.1.0.0">
  <description>converts blast xml or tabular results to a JBrowse-compatible file</description>
  <macros>
    <import>macros.xml</import>

  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
'$__tool_directory__/blast_to_gff3.py'
'$input_type.blast_input'
#if $input_type.input_type_selector == "xml":
  --blastxml
#elif $input_type.input_type_selector == "tsv":
  --blasttab
#end if
> $output]]></command>
  <inputs>
    <conditional name="input_type">
      <param name="input_type_selector" type="select" label="Choose BlastN File Format">
        <option value="xml" selected="true">BlastXML</option>
        <option value="tsv">Blast 25 Column Table"</option>
      </param>
      <when value="xml">
        <param name="blast_input" type="data" format="xml" label="BlastXML Input"/>
      </when>
      <when value="tsv">
        <param name="blast_input" type="data" format="tabular" label="Blast 25 Column Table"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="gff3" name="output"/>
  </outputs>
  <tests>
    <test>
      <param name="input_type_selector" value="xml"/>
      <param name="blast_input" value="BlastnXmlToGff_In.blastxml"/>
      <output name="output" file="BlastnXmlToGff_Out.gff3"/>
    </test>
    <test>
      <param name="input_type_selector" value="tsv"/>
      <param name="blast_input" value="BlastnTsvToGff_In.tabular" ftype="tabular"/>
      <output name="output" ftype="gff3">
        <assert_contents>
          <has_line line="##gff-version 3"/>
          <has_n_lines n="3152"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Convert BlastN XML or tabular results into GFF3 format for visualization within JBrowse, please be sure to select the correct input option for your data. 
This is critical for displaying the position of high-scoring pairs of the Target aligned against the Query. If you need to convert BlastP results, please use the "BlastP Results to GFF3" tool.

]]></help>
  <expand macro="citations"/>
</tool>