<tool id="phage_coast_search" name="PhageCOAST - Search" version="0.2.0">
    <description>Run a new job, and identify the closest proteomes</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <expand macro="requirements"/>
    </requirements>
    <command><![CDATA[
        coast search
        "$db"
        @QUERY@
        --engine blast
        --inplace_workspace
        @QUERY_KEYWORDS@
        @BLAST_TAX_FILTER@
        @BLAST_ALN_OPTIONS@
        @GENERIC_ALN_OPTIONS@
        --web 'http://rosalind.di.uminho.pt:6082/'
        --email phage@coast.um
        && coast report
        "blast_results.tab"
        @QUERY@
        @AAI_FILTER@
        @OUTPUT_FORMAT@
        @QUERY_KEYWORDS@
    ]]></command>
    <inputs>
        <expand macro="input_query" />
        <expand macro="merlin_db_selection"/>
        <expand macro="blast_taxon_filter"/>
        <expand macro="output_format"/>
        <expand macro="aai_filter"/>
        <section name="aln_adv" title="Advanced Alignment Settings" >
            <expand macro="blast_aln_options"/>
            <expand macro="generic_aln_options"/>
        </section>
    </inputs>
    <outputs>
        <expand macro="results_alignment"/>
        <expand macro="results_report"/>
    </outputs>
    <tests>
    </tests>
    <help>

@TIME_WARNING@

PhageCOAST
==========

@GENERAL_DESC@

PhageCOAST is COAST adapted for the Phage Toolkit. The current build uses BLASTp as the search backend tool.

@AAI_DESC@
@TAX_FILTER_WARNING@
@OUT_DESC@

    </help>
    <citations>
        <expand macro="citations_coast"/>
        <expand macro="citations_blast"/>
    </citations>
</tool>