comparison abims_xcms_fillPeaks.xml @ 33:ea611367e1da draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 49203f8a5271fa5e6bb889e907df71ebf7757309

32:565693681374

        @COMMAND_LOG_EXIT@

    ]]></command>

    <inputs>
        <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />

        <section name="Adv" title="Advanced Options" expanded="False">
            <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." />

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

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

**Version 3.0.0.0 - 14/02/2018**

- UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlining codes and methods

- UPDATE: since xcms 3.0.0, the selection of a method is no more needed (chrom or MSW)

- UPDATE: since xcms 3.0.0, new parameters are available: expandMz, expandRt and ppm

**Version 2.1.1 - 29/11/2017**

- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C

**Version 2.1.0 - 07/02/2017**

- IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)

- IMPROVEMENT: xcms.fillpeaks can deal with merged individual data

**Version 2.0.8 - 22/12/2016**

- IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate

**Version 2.0.7 - 06/07/2016**

- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0

**Version 2.0.6 - 04/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies

**Version 2.0.5 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- UPDATE: refactoring of internal management of inputs/outputs

33:ea611367e1da

        @COMMAND_LOG_EXIT@

    ]]></command>

    <inputs>
        <param name="image" type="data" format="rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from groupChromPeaks" />

        <section name="Adv" title="Advanced Options" expanded="False">
            <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." />

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

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

- UPDATE: since xcms 3.0.0, new parameters are available: expandMz, expandRt and ppm


**Version 2.1.1 - 29/11/2017**

- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C


**Version 2.1.0 - 07/02/2017**

- IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)

- IMPROVEMENT: xcms.fillpeaks can deal with merged individual data


**Version 2.0.8 - 22/12/2016**

- IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate


**Version 2.0.7 - 06/07/2016**

- UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0


**Version 2.0.6 - 04/04/2016**

- TEST: refactoring to pass planemo test using conda dependencies


**Version 2.0.5 - 10/02/2016**

- BUGFIX: better management of errors. Datasets remained green although the process failed

- UPDATE: refactoring of internal management of inputs/outputs