comparison abims_xcms_xcmsSet.xml @ 25:dc4d3e2b9968 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit e1f22c9b6d39de7aabc6bb625f65aa5ba6a91312

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            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.raw" label="xset.RData" />
        <data name="sampleMetadata" format="tabular" label="sampleMetadata.tsv" />
        <data name="ticsRawPdf"   format="pdf" label="xset.TICs_raw.pdf" />
        <data name="bpcsRawPdf"   format="pdf" label="xset.BPCs_raw.pdf" />
        <data name="log" format="txt" label="xset.log.txt" />
    </outputs>

    <tests>
        <!--<test>
            <param name="inputs|input" value="zip_file" />
            <param name="inputs|zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
            <param name="methods|method" value="matchedFilter" />
            <param name="methods|step" value="0.01" />
            <param name="methods|fwhm" value="4" />
            <param name="methods|options_m|option" value="show" />
            <param name="methods|options_m|max" value="50" />

                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="inputs|input" value="zip_file" />
            <param name="inputs|zip_file" value="sacuri_current_root.zip"  ftype="zip" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

                </assert_contents>
            </output>
        </test>
        <!-- Passed but disable to save time for Travis" -->
        <!--<test>
            <param name="inputs|input" value="single_file" />
            <param name="inputs|single_file" value="ko15.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="inputs|input" value="single_file" />
            <param name="inputs|single_file" value="ko16.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="inputs|input" value="single_file" />
            <param name="inputs|single_file" value="wt15.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

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            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.raw" label="${input.name.rsplit('.',1)[0]}.xset.RData" />
        <data name="sampleMetadata" format="tabular" label="${input.name.rsplit('.',1)[0]}.sampleMetadata.tsv">
            <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter>
        </data>
        <data name="ticsRawPdf"   format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.TICs_raw.pdf" />
        <data name="bpcsRawPdf"   format="pdf" label="${input.name.rsplit('.',1)[0]}.xset.BPCs_raw.pdf" />
        <data name="log" format="txt" label="${input.name.rsplit('.',1)[0]}.xset.log.txt" />
    </outputs>

    <tests>
        <!--<test>
            <param name="input" value="sacuri_dir_root.zip"  ftype="zip" />
            <param name="methods|method" value="matchedFilter" />
            <param name="methods|step" value="0.01" />
            <param name="methods|fwhm" value="4" />
            <param name="methods|options_m|option" value="show" />
            <param name="methods|options_m|max" value="50" />

                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="sacuri_current_root.zip"  ftype="zip" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

                </assert_contents>
            </output>
        </test>
        <!-- Passed but disable to save time for Travis" -->
        <!--<test>
            <param name="input" value="ko15.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="ko16.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>

                    <has_text text="Sample classes: ." />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="wt15.CDF"  ftype="netcdf" />
            <param name="methods|method" value="centWave" />
            <param name="methods|ppm" value="25" />
            <param name="methods|peakwidth" value="20,50" />
            <output name="log">
                <assert_contents>