<tool id="mspurity_averagefragspectra" name="msPurity.averageFragSpectra" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
    <description>Average and filter LC-MS/MS fragmentation spectra (Inter, Intra or All)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/averageFragSpectra.R'
            --out_rdata='$averageFragSpectra_output_rdata'
            --out_peaklist='$averageFragSpectra_output_tsv'
            --pa='$pa'
            --av_level=$av_level
            --cores=\${GALAXY_SLOTS:-4}
            --minfrac=$minfrac
            --minnum=$minnum
            --ppm=$ppm
            --snr=$snr
            --ra=$ra
            --av=$av
            $sumi
            $rmp
    ]]></command>
    <inputs>
        <param argument="--pa" type="data" label="purityA object" format="rdata"
               help="purityA object saved as 'pa' in a RData file (output from frag4feature tool)"/>


        <param argument="--av_level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
            <option value="intra" selected="true">within a MS data file</option>
            <option value="inter">across MS data files</option>
            <option value="all">within and across MS data files (ignoring intra and inter relationships)</option>
        </param>


        <param argument="--snr" type="float" min="0.0" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
        <param argument="--ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
        <param argument="--minfrac" type="float" min="0.0" max="1.0" value="0.5" label="Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in." help="" />
        <param argument="--minnum" type="integer" min="1" value="1" label="Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor)." help="" />
        <param argument="--ppm" type="float" min="0.0" value="5.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in parts per million." />
        <param argument="--sumi" type="boolean" checked="false" truevalue="--sumi" falsevalue="" label="Sum intensities across (averaged) scans?"   help="" />
        <param argument="--av" type="select" label="Function to calculate the average intensity, m/z and SNR values across (averaged) scans after filtering." help="This is ignored for intensities when intensities are summed." >
            <option value="median" selected="true">median</option>
            <option value="mean">mean</option>
        </param>

        <param argument="--rmp" type="boolean" checked="true" truevalue="--rmp" falsevalue="" label="Remove peaks that do not meet the filtering criteria. Otherwise peaks will be flagged instead."
           help="" />
    </inputs>
    <outputs>
        <data name="averageFragSpectra_output_rdata" format="rdata" label="${tool.name} (${av_level}) on ${on_string}: RData" />
        <data name="averageFragSpectra_output_tsv" format="tsv" label="${tool.name} (${av_level}) on ${on_string}: peaklist" />
    </outputs>
    <tests>
        <test>
            <param name="av_level" value="intra" />
            <param name="pa" value="filterFragSpectra_output.RData" />
            <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_intra.RData" ftype="rdata" compare="sim_size" />
            <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_intra.tsv" ftype="tsv" />
        </test>
        <test>
            <param name="av_level" value="inter" />
            <param name="pa" value="averageFragSpectra_output_intra.RData" />
            <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_inter.RData" ftype="rdata" compare="sim_size" />
            <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_inter.tsv" ftype="tsv" />
        </test>
        <test>
            <param name="av_level" value="all" />
            <param name="pa" value="frag4feature_output.RData" />
            <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_all_only.RData" ftype="rdata" compare="sim_size" />
            <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_all_only.tsv" ftype="tsv" />
        </test>
        <test>
            <param name="av_level" value="all" />
            <param name="pa" value="averageFragSpectra_output_inter.RData" />
            <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_all.RData" ftype="rdata" compare="sim_size" />
            <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_all.tsv" ftype="tsv" />

        </test>
    </tests>

    <help><![CDATA[
=============================================================
Average Fragmentation Spectra
=============================================================
-----------
Description
-----------

Average and filter fragmentation spectra for each XCMS feature using an msPurity purityA object.

The tool uses the msPurity functions averageAllFragSpectra, averageIntraFragSpectra and
averageInterFragSpectra.

The fragmentation spectra can be averaged in multiple ways; intra will average fragmentation
spectra within an mzML file, inter will average fragmentation spectra across mzML files
(requires intra to be run first) and all will average all spectra ignoring the intra and
inter relationships.

The averaging is performed using hierarchical clustering of the m/z values of each peaks,
where m/z values within a set ppm tolerance will be clustered. The clustered peaks are then
averaged (or summed).

The fragmentation can be filtered on the averaged spectra (with the arguments snr, rsd, minfrac, ra)


See Bioconductor documentation for more details, functions:
msPurity::averageIntraFragSpectra()
msPurity::averageInterFragSpectra()
msPurity::averageAllFragSpectra()

-----------
Outputs
-----------
* average_x_fragmentation_spectra_rdata

    ]]></help>

<expand macro="citations" />

</tool>