<tool id="edu.tamu.cpt.blastp_to_gff3" name="BlastP Results to GFF3" version="19.1.0.0">
  <description>converts blast xml results to a JBrowse-compatible file</description>
  <macros>
    <import>macros.xml</import>
    <import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
'$__tool_directory__/blast_to_gff3.py'
'$input_type.blast_input'
#if $input_type.input_type_selector == "xml":
  --blastxml
  '$input_type.include_seq'
#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 BlastP 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"/>
        <param name="include_seq" type="boolean" label="Include protein alignment in Blast view in Apollo/JBrowse" truevalue="--include_seq" falsevalue=""/>
      </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="BlastpXmlToGff_In.blastxml" ftype="xml"/>
      <param name="include_seq" value="false"/>
      <output name="output" file="BlastpXmlToGff_Out.gff3" ftype="gff3"/>
    </test>
    <test>
      <param name="input_type_selector" value="xml"/>
      <param name="blast_input" value="BlastpXmlToGff_In.blastxml" ftype="xml"/>
      <param name="include_seq" value="true"/>
      <output name="output" file="BlastpXmlToGff_OutWithSeq.gff3" ftype="gff3"/>
    </test>
    <test>
      <param name="input_type_selector" value="tsv"/>
      <param name="blast_input" value="BlastpTabToGff_In.tabular" ftype="tabular"/>
      <param name="include_seq" value="false"/>
      <output name="output" ftype="gff3">
        <assert_contents>
          <has_line line="##gff-version 3"/>
          <has_n_lines n="122"/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[
**What it does**

Convert BlastP 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 BlastN results, please use the "BlastN Results to GFF3" tool.

**Options::**

By selecting **Include protein alignment…**, the actual sequence alignment will be displayed 
in the pop-up BLAST view in Apollo/JBrowse. This option currently only works when using XML input.

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