comparison abims_xcms_xcmsSet.xml @ 7:451ff602a957 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29

6:0888f7ef739a

        <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" />

                    <has_text text="Peaks: 59359 (about 14840 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <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" />

                    <has_text text="Peaks: 1535 (about 384 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: bio, blank" />
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[

7:451ff602a957

        <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" />

                    <has_text text="Peaks: 59359 (about 14840 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <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" />

                    <has_text text="Peaks: 1535 (about 384 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <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="faahKO_reduce.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>
                    <has_text text="object with 4 samples" />
                    <has_text text="Time range: 2506.1-4477.9 seconds (41.8-74.6 minutes)" />
                    <has_text text="Mass range: 200.1-600 m/z" />
                    <has_text text="Peaks: 9251 (about 2313 per sample)" />
                    <has_text text="Peak Groups: 0" />
                    <has_text text="Sample classes: KO, WT" />
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[