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<tool id="blast_report_basic" name="BLAST report" version="0.1.0+galaxy0" >
    <description>Produce an HTML table report of BLAST results</description>
    <command>
        <![CDATA[
          python '${__tool_directory__}/blast_report.py' 
            --min-identity ${min_identity}
            --filter-keywords '${filter_keywords}'
            $discard_redundant
            '${tabular_blast_report_input}'
            '${__tool_directory__}/templates/template2.tmpl'
            '${out_html}'
            '${out_tab}'
	    #if str($reference_database_bins) != "None"
	      #for $name, $path in zip(str($reference_database_bins.fields.name).split(','), str($reference_database_bins.fields.path).split(',')):
                -b '${name}' '${path}'
	      #end for
            #end if
        ]]>
    </command>
    <inputs>
        <param name="tabular_blast_report_input" type="data" format="tabular" label="Tabular BLAST results (extended 25 columns + qcov)"/>
        <param name="min_identity" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
        <param name="filter_keywords" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
        <param name="reference_database_bins" type="select" label="Reference Database Bins" multiple="true" display="checkboxes">
            <options from_data_table="blast_report_reference_database_bins">
                <validator type="no_options" message="No BLAST reference bins available" />
            </options>
        </param>
       	<param name="discard_redundant" type="boolean" truevalue="-r" falsevalue="" label="Throw out redundant hits?"/> 
    </inputs>
    <outputs>
        <data name="out_html" format="html" label="$tool.name on data $tabular_blast_report_input.hid: report"/>
        <data name="out_tab" format="tabular" label="$tool.name on data $tabular_blast_report_input.hid: tabular results"/>
    </outputs>
    <tests>
        <test>
	    <param name="reference_database_bins" value="test_entry"/>
	    <param name="tabular_blast_report_input" value="NR_114042.1_vs_NCBI16SMicrobial_top20_standard25col_plus_qcovs.tsv"/>
            <output name="out_tab" file="NR_114042.1_vs_NCBI16SMicrobial_output_report_tabular.tsv" ftype="tabular"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**What it does**

This tool produces a HTML report for each query in a tabular BLAST file.

----

**Tabular BLAST results**

One or more query's BLAST results in extended 26 column tabular format. 

----

**Report template**

The report template dictates the format of the HTML report.
Note that changing the template from the standard "Top 20 hits shown, toggle remainder" to "Euzby results shown first" causes
the order of the results in the HTML report and the tabular BLAST results (if outputted) to be inconsistent with each other.

----

**Minimum percentage identity**

Filter by percentage identity. This filter is applied before the description keyword filters.

----

**Comma-separated list of description keyword filters**

Filter by description keywords. Do not include spaces (unless your keyword is two words). These are applied
after the percentage identity filter.

----

**Database bins**

Bin the results by accession number into "database bins."

----

**Throw out redundant hits?**

Only the first hit for any accession number will be reported.

    </help>
</tool>