<tool id="mspurity_frag4feature" name="msPurity.frag4feature" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
    <description>
        Assign fragmentation spectra to XCMS features using msPurity
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/frag4feature.R'
            --out_dir=.
            --xset='$xset'
            --pa='$pa'
            --cores=\${GALAXY_SLOTS:-4}
            #if $file_load_conditional.file_load_select=="yes"
                --mzML_files='
                #for $i in $file_load_conditional.input
                    $i,
                #end for
                '
                --galaxy_names='
                #for $i in $file_load_conditional.input
                    $i.name,
                #end for
                '
            #end if
            #if $useGroup
                --useGroup
            #end if

            --ppm=$ppm
            --plim=$plim
            #if $intense
                --intense
            #end if
            #if $convert2RawRT
                --convert2RawRT
            #end if


    ]]></command>
    <inputs>

        <param argument="--xset" type="data"  label="xcmsSet object" 
               help="grouped xcmsSet object saved as 'xset' in an RData file"
               format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
        <param argument="--pa" type="data" label="purityA object" format="rdata"
               help="purityA object generated from msPurity_purityA.
               Contains details of fragmentation spectra and precursor ion purity results
               (output from purityA tool)"/>
        <param argument="--ppm" type="float" value="10"
               label="ppm error tolerance between precursor mz and XCMS feature mz"
               help="Fragmentation will be ignored if the precursor mz value is not within
               the ppm error tolerance to the XCMS feature mz"/>
        <param argument="--plim" type="float" label="Precursor ion purity threshold"
               value="0" max="1" min="0" 
               help="Fragmentation will be ignore if the precursor ion purity is less than the
               threshold (further filtering on the precursor ion purity can be done at the averaging
               stage if required)."/>
        <param argument="--intense" type="boolean" checked="true"  
               label="Should the most intense precursor be used within the isolation window?"
               help="If TRUE the most intense precursor will be used. If FALSE the precursor
               closest to the center of the isolation window will be used"/>
        <param  argument="--convert2RawRT" type="boolean" checked="false" 
               label="Was retention time correction used?"
               help="If retention time correction has been used in XCMS set this to yes"/>
        <param argument="--useGroup" type="boolean" checked="false"  
              label="For matching fragmentation to a feature, use the grouped feature range"
              help="For special cases where the MS2 files have no MS1 data or if the MS1 data in the MS2 file is unreliable"  />

        <expand macro="fileload" />

    </inputs>
    <outputs>
        <data name="frag4feature_output_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
              from_work_dir="frag4feature_output.tsv" />
        <data name="frag4feature_output_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
              from_work_dir="frag4feature_output.RData" />
    </outputs>
    <tests>
        <test>
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes"/>
                <param name="input" >
                    <collection type="list">
                        <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
                        <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
                        <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
                        <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
                    </collection>
                </param>
            </conditional>
            <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
            <param name="pa" value="purityA_output.RData"/>
            <output name="frag4feature_output_tsv" value="frag4feature_output.tsv"/>
            <output name="frag4feature_output_rdata" value="frag4feature_output.RData" ftype="rdata" compare="sim_size"/>
        </test>
    </tests>

    <help><![CDATA[
=============================================================
Link fragmentation spectra to XCMS features
=============================================================
-----------
Description
-----------

**General**

Tool to Assign fragmentation spectra (MS/MS) stored within a purityA class object to grouped features within an XCMS xset object.

Please note that the xcmsSet object needs to have been grouped.

The data inputs are:

* A purityA object (generated from purityA) saved in an rdata file.
* A xcmsSet grouped object (generated from xcms_group) saved in an rdata file
* [optional] a dataset collection of the mzML files to resubmit

XCMS calculates individual chromatographic peaks for each mzML file (saved in xset@peaks), these are then grouped together
(using xcms.group). Ideally the mzML files that contain the MS/MS spectra also contain sufficient MS1 scans for XCMS to detect
MS1 chromatographic features. If this is the case, to determine if a MS2 spectra is to be linked to an XCMS grouped feature,
the associated acquisition time of the MS/MS event has to be within the retention time window defined for the individual peaks
associated for each file. The precursor m/z value also has to be within the user ppm tolerance to XCMS feature.

See below for representation of the linking (the \*------\* represent a many-to-many relationship) e.g. 1 or more MS/MS events can be
linked to 1 or more individual feature and an individual XCMS feature can be linked to 1 or more grouped XCMS features

* \[grouped XCMS feature - across files\] \*------\*  \[individual XCMS feature - per file\] \*------\*  \[MS/MS spectra\]

Alternatively, if the "useGroup" argument is set to TRUE, the full width of the grouped peak (determined as the minimum rtmin
and maximum rtmax of the all associated individual peaks) will be used. This option should be used if the mzML file with
MS/MS has very limited MS1 data and so individual chromatographic peaks might not be detected with the mzML files containing the
MS/MS data. However, it should be noted this may lead to potential inaccurate linking.

* \[grouped XCMS peaks\] \*------\* \[MS/MS spectra\]

**Example LC-MS/MS processing workflow**


* Purity assessments
    +  (mzML files) -> purityA -> (pa)
* XCMS processing
    +  (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
* Fragmentation processing
    + (xset, pa) -> **frag4feature** -> filterFragSpectra -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)

**Additional notes**

* If using only a single file, then grouping still needs to be performed within XCMS before frag4feature can be used.
* Fragmentation spectra below a certain precursor ion purity can be be removed (see plim argument).
* A SQLite database can be created directly here but the functionality has been deprecated and the createDatabase function should now be used
* Can experience some problems when using XCMS version < 3 and obiwarp retention time correction.

See Bioconductor documentation for more details, function msPurity::frag4feature()

-----------
Outputs
-----------
* frag4feature_rdata: An updated purityA object saved as rdata file with fragmentation-feature links added
* frag4feature_grouped_msms: A flat file of all the XCMS peaks for each grouped feature and the corresponding fragmentation scans
* frag4feature_sqlite: An SQLite database of the data (including fragmentation scans)

    ]]></help>

<expand macro="citations" />

</tool>