comparison abims_xcms_xcmsSet.xml @ 51:44ab040fffa0 draft

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253

50:1c63d9d402e6

<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy0">
    <description>Chromatographic peak detection</description>

    <macros>
        <import>macros.xml</import>
        <import>macros_xcms.xml</import>

    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" />
        <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" />
        <data name="peaklist_out1" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" >
            <filter>methods['method'] == 'CentWave' and (methods['CentWaveAdv']['peaklist'])</filter>
        </data>
        <data name="peaklist_out2" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" >
            <filter>methods['method'] == 'MatchedFilter' and (methods['MatchedFilterAdv']['peaklist'])</filter>
        </data>
    </outputs>

    <tests>

                <has_text text="Peaks: 1311 (about 328 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: KO, WT" />
            </assert_stdout>
        </test>-->
        <test>
            <param name="image" value="ko15-raw.RData" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />

51:44ab040fffa0

<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Chromatographic peak detection</description>

    <macros>
        <import>macros.xml</import>
        <import>macros_xcms.xml</import>

    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" />
        <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" />
        <data name="peaklist_out" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" >
            <filter>methods['method'] in ['CentWave', 'MatchedFilter'] and (methods['CentWaveAdv']['peaklist'])</filter>
        </data>
    </outputs>

    <tests>

                <has_text text="Peaks: 1311 (about 328 per sample)" />
                <has_text text="Peak Groups: 0" />
                <has_text text="Sample classes: KO, WT" />
            </assert_stdout>
        </test>-->
        <test expect_num_outputs="2">
            <param name="image" value="ko15-raw.RData" ftype="rdata" />
            <conditional name="methods">
                <param name="method" value="CentWave" />
                <param name="ppm" value="25" />
                <param name="peakwidth" value="20,50" />