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planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
author dfornika
date Fri, 27 Sep 2019 13:34:45 -0400
parents 40003338a8e8
children 1c1c680c70a0
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<tool id="screen_abricate_report" name="Screen Abricate Report" version="0.1.0">
    <description>Screens an abricate report for genes of interest</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        '${__tool_directory__}/screen_abricate_report.py'
             '${abricate_report}'
             --screening_file '${screening_file.fields.path}'
             --screened_report '${screened_report}'
             --gene_detection_status '${gene_detection_status}'
    ]]></command>
    <inputs>
        <param name="abricate_report" type="data" format="tabular" />
        <param name="screening_file" type="select" format="tabular">
	    <options from_data_table="abricate_report_screening_files">
	        <validator type="no_options" message="No abricate report screening files are available" />
            </options>
	</param>
    </inputs>
    <outputs>
        <data name="screened_report" type="data" format="tabular" label="Screened Abricate Report" />
        <data name="gene_detection_status" type="data" format="tabular" label="Gene Detection Status" />
    </outputs>
    <tests>
        <test>
            <param name="abricate_report" value="abricate_report.tsv"/>
            <param name="screen" value="screen.tsv"/>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>