view sambamba_plugin.xml @ 28:31c42a2c02d3 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 7f250f4b9484eceef360ba62ef519c94b56c0b97

<macros>
    <token name="@SAMBAMBA_COMMAND@"><![CDATA[
        #set $pattern = "finding positions of the duplicate reads in the file"
        @LN_FILES@
    ]]></token>
    <xml name="sambamba_form">
        <param name="input" type="data" format="txt" multiple="true" label="Output of Sambamba markdup" help="It should contain 'finding positions of the duplicate reads in the file'"/>
    </xml>
    <xml name="sambamba_test">
        <test expect_num_outputs="3">
            <repeat name="results">
                <conditional name="software_cond">
                    <param name="software" value="sambamba"/>
                    <param name="input" value="sambamba.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="Sambamba Markdup"/>
                </assert_contents>
            </output>
            <output name="stats">
                <assert_contents>
                    <has_text text="Sample"/>
                    <has_text text="sambamba_markdup-duplicate_rate"/>
                    <has_n_lines n="2"/>
                    <has_n_columns n="2"/>
                </assert_contents>
            </output>
            <output_collection name="plots" type="list" count="0"/>
        </test>
    </xml>
</macros>