<tool id="coast_report" name="COAST - Report generator" version="0.1.2">
    <description>Recreate the report and outputs with different settings</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <expand macro="requirements"/>
    </requirements>
    <command><![CDATA[
        coast report
        "$result_file"
        @QUERY@
        @AAI_FILTER@
        @HYPO_FILTER@
        @OUTPUT@
        @QUERY_KEYWORDS@
        @OUTPUT_FORMAT@
    ]]></command>
    <inputs>
<!--Select the kind of input to be used-->
        <expand macro="input_query" />
        <param name="result_file" type="data" format="tabular" label="Load previous COAST generated alignment file"/>
<!--Outputs selection-->
        <expand macro="output_format"/>
<!--AAI filtering score-->
        <expand macro="aai_filter"/>
        <expand macro="hypothetical_filter"/>
    </inputs>
    <outputs>
        <expand macro="results_report"/>
    </outputs>
    <tests>
        <test>
          <param name="query_file" value="protein.faa" />
          <param name="result_file" value="blast_results.tab" />
          <param name="aai" value="10" />
          <param name="min_cov" value="50" />
          <param name="min_id" value="40" />
<!--          <output name="coast_report" file="report/coast_report.html"  lines_diff="4"/>-->
          <output name="bh_results" file="report/bh_results.tab" />
          <output name="coast_results" file="report/coast_results.tab" />
        </test>
        <test>
          <param name="query_file" value="protein.faa" />
          <param name="result_file" value="blast_results.tab" />
          <param name="aai" value="20" />
          <param name="min_cov" value="30" />
          <param name="min_id" value="30" />
          <param name="hypothetical" value="true" />
<!--          <output name="coast_report" file="report_h/coast_report.html"  lines_diff="4"/>-->
          <output name="bh_results" file="report_h/bh_results.tab" />
          <output name="coast_results" file="report_h/coast_results.tab" />
        </test>
    </tests>
    <help>

@HYPO_FILTER_WARNING@

COAST Report
============

Generate COAST reports and outputs based in different parameters, using the tabular alignment output produced by COAST Search jobs.

@GENERAL_DESC@
@AAI_DESC@
@OUT_DESC@

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