comparison abims_xcms_fillPeaks.xml @ 41:dbe526f13ff3 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989

40:beebef001d7d

<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.0">

    <description>Integrate areas of missing peaks</description>

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

            <param argument="expandMz" type="integer" value="0" label="Value by which the mz width of peaks should be expanded" help="Each peak is expanded in mz direction by ‘expandMz *’ their original mz width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the mz width of the peak resulting in peakswith twice their original size in mz direction (expansion by half mz width to both sides)." />
            <param argument="expandRt" type="integer" value="0" label="Value by which the RT width of peaks should be expanded" help="Each peak is expanded in RT direction by ‘expandRt *’ their original RT width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the RT width of the peak resulting in peakswith twice their original size in RT direction (expansion by half RT width to both sides)."/>
            <param argument="ppm" type="integer" value="0" label="Specifying a ppm by which the mz width of the peak region should be expanded" help="For peaks with an mz width smaller than ‘mean(c(mzmin, mzmax)) * ppm / 1e6’, the ‘mzmin’ will be replaced by ‘mean(c(mzmin, mzmax)) - (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’ and ‘mzmax’ by ‘mean(c(mzmin, mzmax)) + (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’. This is applied before eventually expanding the mz width using the ‘expandMz’ parameter." />
        </section>

        <expand macro="input_peaklist"/>

        <expand macro="input_file_load"/>

    </inputs>

            <output name="variableMetadata" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv" />
            <output name="dataMatrix" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.tsv" />
        </test>-->
        <test>
            <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/>
            <conditional name="peaklist">
                <param name="peaklistBool" value="true" />
                <param name="convertRTMinute" value="false" />
                <param name="numDigitsMZ" value="4" />
                <param name="numDigitsRT" value="1" />
            </conditional>
            <expand macro="test_file_load_single"/>
            <assert_stdout>
                <has_text text="expandMz: 0" />
                <has_text text="expandRt: 0" />
                <has_text text="object with 4 samples" />

---------------------------------------------------

Changelog/News
--------------

**Version 3.0.0.0 - 08/03/2018**

- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.

- UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW). xcms will detect from the data the peak picking method used in findChromPeaks

41:dbe526f13ff3

<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@WRAPPER_VERSION@.2">

    <description>Integrate areas of missing peaks</description>

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

            <param argument="expandMz" type="integer" value="0" label="Value by which the mz width of peaks should be expanded" help="Each peak is expanded in mz direction by ‘expandMz *’ their original mz width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the mz width of the peak resulting in peakswith twice their original size in mz direction (expansion by half mz width to both sides)." />
            <param argument="expandRt" type="integer" value="0" label="Value by which the RT width of peaks should be expanded" help="Each peak is expanded in RT direction by ‘expandRt *’ their original RT width. A value of ‘0’ means no expansion, a value of ‘1’ grows each peak by 1 * the RT width of the peak resulting in peakswith twice their original size in RT direction (expansion by half RT width to both sides)."/>
            <param argument="ppm" type="integer" value="0" label="Specifying a ppm by which the mz width of the peak region should be expanded" help="For peaks with an mz width smaller than ‘mean(c(mzmin, mzmax)) * ppm / 1e6’, the ‘mzmin’ will be replaced by ‘mean(c(mzmin, mzmax)) - (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’ and ‘mzmax’ by ‘mean(c(mzmin, mzmax)) + (mean(c(mzmin, mzmax)) * ppm / 2 / 1e6)’. This is applied before eventually expanding the mz width using the ‘expandMz’ parameter." />
        </section>

        <expand macro="input_peaklist_section"/>

        <expand macro="input_file_load"/>

    </inputs>

            <output name="variableMetadata" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv" />
            <output name="dataMatrix" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.tsv" />
        </test>-->
        <test>
            <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/>
            <section name="peaklist">
                <param name="peaklistBool" value="true" />
                <param name="convertRTMinute" value="false" />
                <param name="numDigitsMZ" value="4" />
                <param name="numDigitsRT" value="1" />
            </section>
            <expand macro="test_file_load_single"/>
            <assert_stdout>
                <has_text text="expandMz: 0" />
                <has_text text="expandRt: 0" />
                <has_text text="object with 4 samples" />

---------------------------------------------------

Changelog/News
--------------

**Version 3.0.0.2 - 09/11/2018**

- BUGFIX: issue when the vector at peakidx is too long and is written in a new line during the export of the peaklist


**Version 3.0.0.1 - 09/10/2018**

- IMPROVEMENT: the export of the PeakList is now mandatory


**Version 3.0.0.0 - 08/03/2018**

- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed.

- UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW). xcms will detect from the data the peak picking method used in findChromPeaks