<tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="3.12.0+galaxy0">

    <description>Remove or merge chromatographic peaks based on specific criteria.</description>

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

    <expand macro="requirements"/>

    <expand macro="stdio"/>

    <command><![CDATA[
        @COMMAND_RSCRIPT@/xcms_refine.r
        image '$image'

        method $methods.method
        #if $methods.method == "CleanPeaks":
            maxPeakwidth $methods.maxPeakwidth
        #elif $methods.method == "FilterIntensity":
            threshold $methods.threshold
            nValues $methods.nValues
            value $methods.value
        #else:
            expandRt $methods.expandRt
            expandMz $methods.expandMz
            ppm $methods.ppm
            minProp $methods.minProp
        #end if

        msLevel $msLevel

        @COMMAND_FILE_LOAD@

        @COMMAND_LOG_EXIT@
   ]]></command>

    <inputs>
        <param name="image" type="data" format="rdata.xcms.findchrompeaks" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks" />
        <conditional name="methods">
            <param name="method" type="select" label="Method for peak refinement" help="See the help section below">
                <option value="CleanPeaks" selected="true">CleanPeaks - remove peaks that are too wide</option>
                <option value="FilterIntensity">FilterIntensity - remove peaks with too low intensity</option>
                <option value="MergeNeighboringPeaks">MergeNeighboringPeaks - combine peaks that are too close together</option>
            </param>
            <when value="CleanPeaks">
                <param argument="maxPeakwidth" type="float" value="10" label="MaxPeakWidth" help="maximum peak width in seconds.  See CleanPeaks manual (linked in help below)." />
            </when>
            <when value="FilterIntensity">
                <param argument="threshold" type="float" value="0" label="minimal required intensity" help="minimal required intensity for a peak to be retained.  Defaults to 0.0." />
                <param argument="nValues" type="integer" value="1" label="minimum number of data points per peak" help="number of data points (per chromatographic peak) that have to be >= threshold. Defaults to 1." />
                <param name="value" type="select" label="Definition of peak intensity" help="See the FilterIntensity manual (linked in help below). 'intb' requires centWave processed data">
                    <option value="maxo" selected="true">maxo - use maximum peak intensities</option>
                    <option value="into">into - use integrated peak intensities</option>
                    <option value="intb">intb - use baseline-corrected integrated peak intensities</option>
                </param>
            </when>
            <when value="MergeNeighboringPeaks">
                <param argument="expandRt" type="float" value="2" label="rt expansion (seconds)" help="seconds of expansion of retention time window (on both sides) to check for overlapping peaks. Defaults to 2." />
                <param argument="expandMz" type="float" value="0" label="m/z expansion (m/z units)" help="'m/z units' of expansion of m/z window (on both sides) to check for overlapping peaks. Defaults to 0." />
                <param argument="ppm" type="float" value="10" label="ppm expansion (ppm units)" help="'relative 'm/z units' (in parts per million) of expansion of m/z window (on both sides) to check for overlapping peaks. Defaults to 10." />
                <param argument="minProp" type="float" value="0.75" label="minimum proportion at midpoint" help="See MergeNeighboringPeaks manual (linked in help below).  Minimum proportion midway between peaks relative to the smaller peak's 'maxo' (maximal intensity at peak apex).  Defaults to 0.75." />
            </when>
        </conditional>
        <param argument="msLevel" type="integer" value="1" label="msLevel for refinement" help="the MS level on which refinement should be performed. Defaults to 1." />

        <expand macro="input_file_load"/>
    </inputs>

    <outputs>
        <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.refine.RData" from_work_dir="xcmsSet.RData" />
    </outputs>

    <tests>
        <!--
            test 1 - MergeNeighboringPeaks method
        -->
        <test>
            <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
            <conditional name="methods">
                <param name="method" value="MergeNeighboringPeaks"/>
                <param name="expandRt" value="2" />
                <param name="expandMz" value="0" />
                <param name="ppm" value="10" />
                <param name="minProp" value="0.75" />
            </conditional>
            <expand macro="test_file_load_single"/>
            <assert_stderr>
                <has_text text="Evaluating 547 peaks in file wt15.CDF for merging ... OK" />
                <has_text text="Evaluating 547 peaks in file wt16.CDF for merging ... OK" />
                <has_text text="Evaluating 558 peaks in file ko15.CDF for merging ... OK"/>
                <has_text text="Evaluating 589 peaks in file ko16.CDF for merging ... OK" />
                <has_text text="Merging reduced 9251 chromPeaks to 9093" />
            </assert_stderr>
            <assert_stdout>
                <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: 9093 (about 2273 per sample)" />
            </assert_stdout>
        </test>
        <!--
            test 2 - FilterIntensity method
        -->
        <test>
            <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
            <conditional name="methods">
                <param name="method" value="FilterIntensity"/>
                <param name="threshold" value="1e5" />
                <param name="nValues" value="3" />
                <param name="value" value="into" />
            </conditional>
            <expand macro="test_file_load_single"/>
            <assert_stderr>
                <has_text text="Removed 9018 chromatographic peaks" />
            </assert_stderr>
            <assert_stdout>
                <has_text text="object with 4 samples" />
                <has_text text="Time range: 2657.9-4124.2 seconds (44.3-68.7 minutes)" />
                <has_text text="Mass range: 256.1-599.4 m/z" />
                <has_text text="Peaks: 233 (about 58 per sample)" />
            </assert_stdout>
        </test>
        <!--
            test 3 - CleanPeaks method
        -->
        <test>
            <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
            <conditional name="methods">
                <param name="method" value="CleanPeaks"/>
                <param name="maxPeakwidth" value="8" />
            </conditional>
            <expand macro="test_file_load_single"/>
            <assert_stderr>
                <has_text text="Removed 6037 of 9251 chromatographic peaks" />
            </assert_stderr>
            <assert_stdout>
                <has_text text="object with 4 samples" />
                <has_text text="Time range: 2524.9-4473.2 seconds (42.1-74.6 minutes)" />
                <has_text text="Mass range: 200.2-600 m/z" />
                <has_text text="Peaks: 3214 (about 804 per sample)" />
            </assert_stdout>
        </test>
    </tests>

    <help><![CDATA[

.. class:: infomark

**Authors**  Johannes Rainer Johannes.Rainer@eurac.edu and Mar Garcia-Aloy mar.garcia@fmach.it

@HELP_AUTHORS_WRAPPERS@

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


=====================
xcms refineChromPeaks
=====================

-----------
Description
-----------

After peak identification with xcms findChromPeaks (xcmsSet), this tool refines those peaks.
It either removes peaks that are too wide or removes peaks with too low intensity or combines peaks that are too close together.

Note well that refineChromPeaks methods will always remove feature definitions,
because a call to this method can change or remove identified chromatographic peaks, which may be part of features.
Therefore it must only be run immediately after findChromPeaks (xcmsSet).

-----------------
Workflow position
-----------------

**Upstream tools**

==================================== ======================== ==============================
Name                                 Output file              Format
==================================== ======================== ==============================
xcms.findChromPeaks Merger (single)  xset.merged.RData        rdata.xcms.findchrompeaks
------------------------------------ ------------------------ ------------------------------
xcms.findChromPeaks (zip)            ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
==================================== ======================== ==============================


**Downstream tools**

==================================== ======================== =========================
Name                                 Output file              Format
==================================== ======================== =========================
xcms.findChromPeaks Merger (single)  ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
------------------------------------ ------------------------ -------------------------
xcms.groupChromPeaks (zip)           ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
==================================== ======================== =========================

**General schema of the metabolomic workflow**

This tool would appear between findChromPeaks and group, but only when the choice of peaks needs to be refined, e.g., to accommodate HILIC data.

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

----------
Parameters
----------

Method to use for refinement
----------------------------

**CleanPeaks**

    | Remove chromatographic peaks with too large rt width.
    | See the CleanPeaks_manual_

**FilterIntensity**

    | Remove chromatographic peaks based on intensity.
    | See the FilterIntensity_manual_

**MergeNeighboringPeaks**

    | Merge neighboring and overlapping chromatographic peaks.
    | See the MergeNeighboringPeaks_manual_

.. _CleanPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-clean.html
.. _FilterIntensity_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-filter-intensity.html
.. _MergeNeighboringPeaks_manual: https://rdrr.io/bioc/xcms/man/refineChromPeaks-merge.html

@HELP_XCMS_MANUAL@

------------
Output files
------------

xset.RData: rdata.xcms.findchrompeaks format

    | (single) RData files that are necessary in the second step of the workflow "xcms.groupChromPeaks" - must be merged first using "xcms.findChromPeaks Merger"
    | (zip) RData file that is necessary in the second step of the workflow "xcms.groupChromPeaks".


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

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

.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS


**Version 3.6.1.0 - 08/02/2021**

- NEW: first version of tool wrapper


    ]]></help>

    <citations>
      <citation type="doi">10.5281/zenodo.3909299</citation>
      <expand macro="citation_w4m"/>
      <citation type="doi">10.1021/ac051437y</citation>
    </citations>


</tool>