view blast2html.xml @ 120:2729c2326235

Fix for Rikilt issue 13 Hit e-value and identity% should be taken from the hsp with the highest bit score. Previously each of these values was calculated independently. Also use arrays for cover calculation instead of python lists and refactor the hit_info() code a bit.

<tool id="blast2html" name="blast2html" version="0.0.14">
    
    <description>Convert BLAST XML to HTML</description>
    
    <requirements>
      <requirement name="package" version="0.2">blast2html_venv</requirement>
    </requirements>
    
    <command interpreter="python">blast2html.py -i "${input}" -o "${output}" --db-config-dir "${GALAXY_DATA_INDEX_DIR}"</command>

    <stdio>
      <!-- Any exit code other than 0 is an error -->
      <exit_code range="1:" />
      <exit_code range=":-1" />
    </stdio>
    
    <inputs>
        <param format="blastxml" name="input" type="data" label="Source file"/>
    </inputs>
    
    <outputs>
        <data format="html" name="output" />
    </outputs>
    
    <tests>
        <test>
            <param name="input" value="blast xml example1.xml"/>
            <output name="output" file="blast xml example1.html"/>
        </test>
        <test>
            <param name="input" value="blast xml example2.xml"/>
            <output name="output" file="blast xml example2.html"/>
        </test>
        <test>
            <param name="input" value="blast xml example3.xml"/>
            <output name="output" file="blast xml example3.html"/>
        </test>
        <test>
            <param name="input" value="blast xml example4.xml"/>
            <output name="output" file="blast xml example4.html"/>
        </test>
    </tests>
    
    <help>
        This tool converts the default BLAST XML result into a HTML document
    </help>
    
</tool>