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<tool id="abricate" name="ABRicate" version="0.1.0">
    <requirements>
        <requirement type="package" version="0.3">abricate</requirement>
        <requirement type="package" version="5.18.1">perl</requirement>
        <requirement type="package" version="2.2.31">blast+</requirement>
    </requirements>

    <version_command>abricate --version</version_command>

    <command detect_errors="exit_code"><![CDATA[
        abricate "$fasta_input"
        #if $settings.advanced == "advanced"
            $settings.no_header
            #if $settings.min_dna_id
                --minid=$settings.min_dna_id
            #end if
            #if $settings.cull_limit
                --cull=$settings.cull_limit
            #end if
        #end if
        > "$report"
    ]]></command>

    <inputs>
        <param name="fasta_input" type="data" format="fasta" label="Select fasta file" help="Specify fasta file to screen for antibiotic resistant genes"/>
        <conditional name="settings">
            <param name="advanced" type="select" label="Specify advanced parameters">
                <option value="simple" selected="true">No, use program defaults.</option>
                <option value="advanced">Yes, see full parameter list.</option>
            </param>
            <when value="simple">
            </when>
            <when value="advanced">
                <param name="no_header" type="boolean" label="Suppress header" truevalue="--noheader" falsevalue=""
                  help="Suppress output file's column headings" optional="true" />
                <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="75" min="0" max="100" help="Minimum DNA identity (default 75, must be between 0-100)" optional="true" />
                <param name="cull_limit" type="integer" label="Culling limit" value="1" min="0" help="Culling limit (encompassing hits) (default 1, must be a positive number)" optional="true">
                    <validator type="in_range" message="This value must be greater than or equal to 0" min="0" max="2147483647"/>
                </param>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data format="tabular" name="report" label="${tool.name} on ${on_string} report file"/>
    </outputs>

    <tests>
        <!-- Basic test - will produce no results. -->
        <test>
            <param name="fasta_input" value="Acetobacter.fna"/>
            <param name="advanced" value="simple"/>
            <output name="report" ftype="tabular" file="output_noresults.txt" />
        </test>

        <!-- Basic test - will produce results. -->
        <test>
            <param name="fasta_input" value="MRSA0252.fna"/>
            <param name="advanced" value="simple"/>
            <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
        </test>

        <!-- Advanced test - No header. -->
        <test>
            <param name="fasta_input" value="MRSA0252.fna"/>
            <param name="advanced" value="advanced"/>
            <param name="no_header" value="True"/>
            <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
        </test>

        <!-- Advanced test - Cull limit 100 -->
        <test>
            <param name="fasta_input" value="MRSA0252.fna"/>
            <param name="advanced" value="advanced"/>
            <param name="cull_limit" value="100"/>
            <output name="report" ftype="tabular" file="output_cull100.txt" compare="contains"/>
        </test>

        <!-- Advanced test - Min DNA ID 100 -->
        <test>
            <param name="fasta_input" value="MRSA0252.fna"/>
            <param name="advanced" value="advanced"/>
            <param name="min_dna_id" value="100"/>
            <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
        </test>
    </tests>

    <help><![CDATA[
**What it does**

Given a FASTA contig file, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The database of these genes is built from ResFinder.

**Output**

ABRicate will produce a tab-seperated output file with the following outputs:

+---------------+------------------------------------------------+
|  Column       | Description                                    |
+===============+================================================+
|  FILE         | The filename this hit came from                |
+---------------+------------------------------------------------+
|  SEQUENCE     | The sequence in the filename                   |
+---------------+------------------------------------------------+
|  START        | Start coordinate in the sequence               |
+---------------+------------------------------------------------+
|  END          | End coordinate                                 |
+---------------+------------------------------------------------+
|  GENE         | ABR gene                                       |
+---------------+------------------------------------------------+
|  COVERAGE     | What proportion of the gene is in our sequence |
+---------------+------------------------------------------------+
|  COVERAGE_MAP | A visual represenation                         |
+---------------+------------------------------------------------+
|  GAPS         | Was there any gaps in the                      |
|               | alignment - possible pseudogene?               |
+---------------+------------------------------------------------+
|  %COVERAGE    | Proportion of gene covered                     |
+---------------+------------------------------------------------+
|  %IDENTITY    | Proportion of exact nucleotide matches         |
+---------------+------------------------------------------------+


**Example Output**

::

	#FILE   SEQUENCE    START   END GENE    COVERAGE    COVERAGE_MAP    GAPS    %COVERAGE   %IDENTITY
	Processing: 6008.fna
	Found 12 ABR genes in 6008.fna
	Klebsiella.fna  NC_021232.1 872545  872964  fosA    1-420/420   =============== 0   100.00  100.00
	Klebsiella.fna  NC_021232.1 1381252 1382427 oqxA    1-1176/1176 =============== 0   100.00  99.32
	Klebsiella.fna  NC_021232.1 2584899 2585759 blaSHV1 1-861/861   =============== 0   100.00  99.88


    ]]></help>

    <citations>
      <citation type="bibtex">
        @UNPUBLISHED{Seemann2016,
        author = "Seemann T",
        title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
        year = "2016",
        note = "https://github.com/tseemann/abricate"}
      </citation>
    </citations>
</tool>