view salmonquantmerge.xml @ 5:cfb0849582e1 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"

<tool id="salmonquantmerge" name="Salmon quantmerge" version="@VERSION@">
    <description>Merge multiple quantification results into a single file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        @qmerge@
    ]]></command>
    <inputs>
        <expand macro="quantmerge"/>
    </inputs>
    <outputs>
        <data name="mergedfile" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="qmergeout.tab"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <repeat name="quantfiles">
                <param name="quants" value="quant2.sf"/>
                <param name="names" value="asdf"/>
            </repeat>
            <repeat name="quantfiles">
                <param name="quants" value="quant1.sf"/>
                <param name="names" value="qwerty"/>
            </repeat>
            <output name="mergedfile" ftype="tabular">
                <assert_contents>
                    <has_text text="qwerty"/>
                    <has_text text="NM_014621"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        @salmonhelp@
    ]]></help>
    <expand macro="citations"/>
</tool>