<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">
    </expand>

 <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="Rscript"><![CDATA[
        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 name="pa" type="data" label="purityA object" format="rdata"
               help="purityA object saved as 'pa' in a RData file (output from frag4feature tool)"/>


        <param name="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 name="snr" type="float" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
        <param name="ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
        <param name="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 name="minnum" type="integer" value="1" label="Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor)." help="" />
        <param name="ppm" type="float" value="5.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in parts per million." />
        <param name="sumi" type="boolean" checked="false" truevalue="--sumi" falsevalue="" label="Sum intensities across (averaged) scans?"   help="" />
        <param name="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 name="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>