<tool id="abricate_summary" name="ABRicate Summary" version="@VERSION@" profile="@PROFILE@">
    <description>
        Combine ABRicate results into a simple matrix of gene presence/absence
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='xrefs'/>
    <expand macro='edam_ontology'/>
    <expand macro="requirements" />
    <expand macro="version_command" />

    <command detect_errors="exit_code"><![CDATA[
        mkdir reports &&
        #import re
        #for report in $abricate_reports
          #set $safename = re.sub('[^\w\-_\.]', '_', $report.element_identifier)
          ln -s '$report' 'reports/$safename' &&
        #end for
        cd reports/ &&
        abricate --summary *
        > '$summary'
    ]]></command>

    <inputs>
       <param name="abricate_reports" type="data" multiple="true" format="tabular" label="Abricate output reports to summarize"/>
    </inputs>

    <outputs>
        <data name="summary" format="tabular"/>
    </outputs>

    <tests>
        <test>
            <param name="abricate_reports" value="output_db-card.txt,output_db-megares.txt"/>
            <output name="summary" ftype="tabular" file="output_summary.txt" />
        </test>
    </tests>

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

ABRicate can combine results into a simple matrix of gene presence/absence. An absent gene is denoted by '.' and a present gene is represented by its '%COVERAGE`. This can be individual abricate reports, or a combined one.

**Example Output**

::

        #FILE	NUM_FOUND	AAC3	ANT(4')-Ib	ANT3-DPRIME	ANT4-PRIME	APH3-PRIME	ARLR	ARLS	BLAI	BLAR	BLAZ	BLE	DHAP	ERMA	ErmA	FOSB	LMRS	MECA	MECI	MEPA	MEPB	MEPR	MGRA	NORA	NORB	PC1_beta-lactamase_(blaZ)	RLMH	Staphylococcus_aureus_FosB	Staphylococcus_aureus_norA	Staphylococcys_aureus_LmrS	TET38	arlR	arlS	mecA	mecI	mecR1	mepA	mepR	mgrA	tet(38)
        sample1	15	.	100.00	.	.	.	.	.	.	.	.	.	.	.	100.00;100.00	.	.	.	.	.	.	.	.	.	.	100.00	.	100.00	99.91	100.00	.	100.00	100.00	100.00	100.00	100.00	100.00	100.00	100.00	100.00
        sample2	24	100.00	.	100.00;100.00	100.00	100.00	100.00	100.00	100.00	100.00	100.00	100.00	100.00	100.00;100.00	.	100.00	100.00	100.00;100.00	100.00	100.00	100.00	100.00	100.00	100.00	100.00	.	100.00	.	.	.	100.00	.	.	.	.	.	.	.	.	.

    ]]></help>

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