view psm_eval.xml @ 0:77cc9cc99e15 draft

Initial commit.

<?xml version="1.0"?>
<tool name="Peptide-Spectrum-Matches (PSMs) Evaluation" id="psm_eval" version="0.1.0">
    <requirements>
        <requirement type="package">psm_eval</requirement>
    </requirements>
    <description>Re-evalute potential PSMs using the psm-eval application.</description>
    <command>psm_eval --settings $driver</command>
    <configfiles>
        <configfile name="driver"># YAML driver for PSM Eval
peak_lists:
#for $peak_list in $peak_lists:
  - path: $peak_list
    name: "$peak_list.display_name"
    encoded_id: "${$__app__.security.encode_id( $peak_list.id )}"
#end for
psms: $psms_cond.psms
psms_type: $psms_cond.type
output: $output
output_format: $output_type
mass_type: $mass_type
mass_tolerance: $default_mass_tolerance
columns:
#for $column in $columns
#set $column_options = $column.column
#set $type = str(column_options['type'])
  - type: ${type}
#if $type in ['ions_matched', 'peaks_matched']
    aggregate_by: $column_options.aggregate_by
#if $column_options.tolerance.specify
    mass_tolerance: $column_options.tolerance.tolerance
#end if
#end if
#if $type in ['ions_matched', 'peaks_matched', 'num_peaks']
## Handle peak filters
    peak_filters:
#for $peak_filter in $column_options.peak_filters
#set $peak_filter_options = $peak_filter.peak_filter
#set $peak_filter_type = str(peak_filter_options['peak_filter_type'])
    - type: $peak_filter_type
#if $peak_filter_type in ['percent_tic', 'quantile', 'percent_max_intensity']
      percent: $peak_filter_options.percent
#end if
#if $peak_filter_type == 'quantile'
      q: $peak_filter_options.q
      k: $peak_filter_options.k
#end if
#end for
#end if
#if $type in ['ions_matched', 'peaks_matched']
## Handle ions series
#set $ions = $column_options
    ions:
      series: $ions.ion_series
#if $ions.losses
      losses: $ions.losses
#end if
#end if
#if $type == "source_statistic"
    statistic_name: ${str(column_options['source_statistic'])}
#end if
#if $type == "link"
    link_type: galaxy
#end if
#end for
        </configfile>
    </configfiles>
    <inputs>
        <conditional name="psms_cond">
            <param name="type" type="select" label="PSMs Type" help="">
                <option value="mzid">MzIdentML (mzid)</option>
                <option value="proteinpilot_peptide_report">ProteinPilot Peptide Report</option>
            </param>
            <when value="mzid">
                <param format="mzid" name="psms" type="data" label="MzIdentML containing PSMs" help="" />
            </when>
            <when value="proteinpilot_peptide_report">
                <param format="tabular" name="psms" type="data" label="ProteinPilot Peptide Report" help="" />
            </when>
        </conditional>
        <param format="mzml" name="peak_lists" type="data" label="Peak list (mzML)" multiple="true" help="" />
        <param name="output_type" type="select" label="Output Type" help="">
            <option value="tsv">Tabular (tsv)</option>
            <option value="html">HTML</option>
        </param>
        <param name="default_mass_tolerance" type="float" label="Default Mass Tolerance" value="0.5" />
        <param name="mass_type" type="select" label="Mass Type">
            <option value="monoisotopic" selected="true">Monoisotopic</option>
            <option value="average">Average (has known problems)</option>
        </param>
        <repeat name="columns" title="Column">
            <conditional name="column">
                <param type="select" name="type" label="Column Type">
                    <option value="peptide">Peptide Sequence</option>
                    <option value="scan_index">Scan Index</option>
                    <option value="scan_number">Scan Number</option>
                    <option value="scan_id">Scan ID</option>
                    <option value="scan_source">Peak List</option>
                    <option value="num_peaks">Number of Peaks</option>
                    <option value="peaks_matched">Peaks Matched Statistic</option>
                    <option value="ions_matched">Ions Matched Statistic</option>
                    <option value="total_ion_current">Total Ion Current</option>
                    <option value="source_statistic">Statistic from PSM Source</option>
                    <option value="link">ProtVis Link</option>
                </param>
                <when value="num_peaks">
                    <expand macro="peak_filters" />
                </when>
                <when value="peaks_matched">
                    <param name="aggregate_by" label="Peak Matching Statistic" type="select">
                        <option value="count">Number of Matched Peaks</option>
                        <option value="count_missed">Number of Unmatched Peaks</option>
                        <option value="percent">Percent of Matched Peaks</option>
                        <option value="percent_missed">Percent of Unmatched Peaks</option>
                    </param>
                    <expand macro="ions" />
                    <expand macro="peak_filters" />
                    <expand macro="tolerance_conditional" />
                </when>
                <when value="ions_matched">
                    <param name="aggregate_by" label="Ion Matching Statistic" type="select">
                        <option value="count">Number of Matched Ions</option>
                        <option value="count_missed">Number of Unmatched Ions</option>
                        <option value="count_longest_stretch">Longest Stretch of Matched Ions</option>
                        <option value="percent">Percent of Matched Ions</option>
                        <option value="percent_missed">Percent of Unmatched Ions</option>
                        <option value="list_matches">List Matched Ions</option>
                        <option value="list_misses">List Unmatched Ions</option>
                    </param>
                    <expand macro="ions" />
                    <expand macro="peak_filters" />
                    <expand macro="tolerance_conditional" />
                </when>
                <when value="source_statistic">
                    <param name="source_statistic" label="PSM Source Statistic" type="select">
                        <option value="xcorr">xcorr</option>
                        <option value="MyriMatch:MVH">MyriMatch: MVH</option>
                        <option value="MyriMatch:mzFidelity">MyriMatch: mzFidelity</option>
                        <option value="Conf">Conf</option>
                    </param>
                </when>
                <when value="link">
                </when>
            </conditional>
        </repeat>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="PSM Evaluation of ${on_string}">
            <change_format>
                <when input="output_type" value="html" format="html" />
            </change_format>
        </data>
    </outputs>
    <macros>
        <macro name="ions">
            <param name="ion_series" type="select" multiple="true" label="Ion Series">
                <option value="a1">a1</option>
                <option value="a2">a2</option>
                <option value="a3">a3</option>
                <option value="b1">b1</option>
                <option value="b2">b2</option>
                <option value="b3">b3</option>
                <option value="c1">c1</option>
                <option value="c2">c2</option>
                <option value="c3">c3</option>
                <option value="x1">x1</option>
                <option value="x2">x2</option>
                <option value="x3">x3</option>
                <option value="y1">y1</option>
                <option value="y2">y2</option>
                <option value="y3">y3</option>
                <option value="z1">z1</option>
                <option value="z2">z2</option>
                <option value="z3">z3</option>
                <option value="m1">M1</option>
                <option value="m2">M2</option>
                <option value="internal">Internal Ions</option>
            </param>
            <param name="losses" type="select" multiple="true" label="Losses" value="">
                <option value="H2O">H2O</option>
                <option value="NH3">NH3</option>
                <option value="CO">CO (-28) on internal ions</option>
            </param>
        </macro>
        <macro name="tolerance_conditional">
            <conditional name="tolerance">
                <param name="specify" label="Specify Mass Tolerance" type="boolean" />
                <when value="false">
                </when>
                <when value="true">
                    <param name="tolerance" value="0.5" label="Tolerance" type="float" />
                </when>
            </conditional>
        </macro>
        <!--
        <macro name="conditional_ions">
            <conditional name="specify_ions">
                <param type="boolean" truevalue="true" falsevalue="false" name="specify" label="Specify Ions?" />
                <when value="true">
                    <expand macro="ions" />
                </when>
                <when value="false" />
            </conditional>
        </macro>
        -->
        <macro name="peak_filters">
            <repeat name="peak_filters" title="Peak Filter">
                <expand macro="peak_filter" />
            </repeat>
        </macro>
        <macro name="peak_filter">
            <conditional name="peak_filter">
                <param type="select" label="Filter Peaks on" name="peak_filter_type">
                    <option value="percent_tic">Intensity as a Percent of Total Ion Current</option>
                    <option value="quantile">Intensity Quantile</option>
                    <option value="percent_max_intensity">Intensity as a Percent of Maximum Spectrum Peak Intensity</option>
                </param>
                <when value="percent_tic">
                    <expand macro="percent_param" />
                </when>
                <when value="percent_max_intensity">
                    <param name="percent" label="Percent of Maximum Peak Intensity" type="float" value="0.1" />
                </when>                
                <when value="quantile">
                    <param name="q" label="q" type="integer" help="q is the number of partitions to break intensity into, k is the position to pull from. For instance if q=2 and k=1, the peaks above the median intensity will be used and if q=3 and k=2, the middle third of peaks by intensity will be used." value="2" />
                    <param name="k" label="k" type="integer" value="1"/>
                    <expand macro="percent_param" />
                </when>
            </conditional>
            <!-- TODO: Add m/z, intensity thresholds. -->
        </macro>
        <macro name="percent_param">
            <param name="percent" label="Percent TIC Threshold" type="float" help="Filter all peaks whose intensity does not exceed this percent of total ion current." value="0.02" />
        </macro>
    </macros>
</tool>