view bamtools_plugin.xml @ 24:f7e2f1eb3a16 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit dffbb5d421a5a5773bcb7f05933b12c45461bb58
author iuc
date Mon, 02 Sep 2024 14:22:54 +0000
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<macros>
    <token name="@BAMTOOLS_COMMAND@"><![CDATA[
        #set $pattern = "Stats for BAM file(s)"
        @LN_FILES@
    ]]></token>
    <xml name="bamtools_form">
        <param name="input" type="data" format="txt" multiple="true" label="Output of BAMtools" help="It should contain 'This file was produced by bcftools stats'"/>
    </xml>
    <xml name="bamtools_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="bamtools"/>
                    <param name="input" value="bamtools.txt"/>
                </conditional>
            </repeat>
            <param name="title" value="Title of the report"/>
            <param name="comment" value="Commment for the report"/>
            <param name="flat" value="true"/>
            <param name="export" value="true"/>
            <output name="html_report">
                <assert_contents>
                    <has_text text="Title of the report"/>
                    <has_text text="Commment for the report"/>
                    <has_text text="bamtools-stats"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="bamtools_txt"/>
                    <has_text text="Bamtools"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="1"/>
        </test>
    </xml>
</macros>