comparison psm_eval.xml @ 3:91fb73c8619c draft default tip

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<?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

  - path: $peak_list
    name: "$peak_list.display_name"
    encoded_id: "${$__app__.security.encode_id( $peak_list.id )}|${$peak_list.extra_dir_file_name if hasattr($peak_list, 'extra_dir_file_name') else ''}"
#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:

#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

#end for
        </configfile>
    </configfiles>
    <inputs>
        <conditional name="psms_cond">
            <param name="type" type="select" label="PSMs Type" help="ProteinPilot Peptide Report inputs results from ProteinPilot search algorithm. mzidentML inputs results from an open source search algorithm">
                <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="select appropriate file from history" />
            </when>
            <when value="proteinpilot_peptide_report">
                <param format="tabular" name="psms" type="data" label="ProteinPilot Peptide Report" help="select appropriate file from history" />
            </when>
        </conditional>
        <param format="mzml" name="peak_lists" type="data" label="Peak list (mzML)" multiple="true" help="select MZML file of experimental MS/MS data" />
        <param name="output_type" type="select" label="Output Type" help="Tabular is a spreadsheet containing columns of selected properties listed below. (select tabular as the output type and Peptide sequence as the column type. HTML provides visualization of matches (select HTML as the output type and ProtVis Link as the column type)">
            <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" help="error of precursor ion (in Da). Recommended: 0.5 for LTQ/Orbitrap instrument; 0.01 for HCD/Orbitrap acquisition" />
        <param name="mass_type" type="select" label="Mass Type" help="Monoisotopic: selects most abundant isotopic MS peak for theoretical mass calculation. Average: uses average mass values for theoretical mass calculation">
            <option value="monoisotopic" selected="true">Monoisotopic</option>
            <option value="average">Average (has known problems)</option>
        </param>
        <repeat name="columns" title="Column">
            <conditional name="column">

            <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>
    <help>
**What it does**

Generates user-selected metrics in a tabular format for peptide-spectral matches using spectral/peptide summary generated from the search algorithm and mzml input files. The tabular format that is generated can be used for filtering based on user-defined thresholds. Alternatively, it can also provide visualization of peptide-spectral matches, thus allowing further metrics evaluation.
<help>
</tool>

3:91fb73c8619c

<?xml version="1.0"?>
<tool name="Peptide-Spectrum-Matches (PSMs) Evaluator" id="psm_eval" version="0.1.0">
    <requirements>
        <requirement type="package" version="22">binaries_for_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

  - path: $peak_list
    name: "$peak_list.display_name"
    encoded_id: "${$__app__.security.encode_id( $peak_list.id )}|${$peak_list.extra_dir_file_name if hasattr($peak_list, 'extra_dir_file_name') else ''}"
#end for
psms: $psms_cond.psms
#set $psms_type = $psms_cond.type
#if $psms_type == "tpp_derived_report"
scan_id_column_index: ${int(str($psms_cond.scan_id_column)) - 1}
scan_source_column_index: ${int(str($psms_cond.scan_source_column)) - 1}
peptide_column_index: ${int(str($psms_cond.peptide_column)) - 1}
#end if
psms_type: $psms_cond.type

output: $output
output_format: $output_type
mass_type: $mass_type
mass_tolerance: $default_mass_tolerance
columns:

#end if
#if $peak_filter_type == 'quantile'
      q: $peak_filter_options.q
      k: $peak_filter_options.k
#end if
#if $peak_filter_type in ['mz_range_absolute', 'mz_range_percent_bp']
      min: $peak_filter_options.min
      max: $peak_filter_options.max
#end if
#end for
#end if
#if $type in ['ions_matched', 'peaks_matched']
## Handle ions series
#set $ions = $column_options

#end for
        </configfile>
    </configfiles>
    <inputs>
        <conditional name="psms_cond">
            <param name="type" type="select" label="PSMs Type" help="ProteinPilot Peptide Report inputs results are generated from the &quot;Convert ProteinPilot Group to Tabular&quot; tool. mzidentML inputs (beta) result from many search tools. Currently only MyriMatch has been tested, and with only one input file">
                <option value="mzid">MzIdentML (mzid)</option>
                <option value="proteinpilot_peptide_report">ProteinPilot Peptide Report</option>
                <option value="tpp_derived_report">Trans-Proteomic Pipeline Derived Peptide Report</option>
            </param>
            <when value="mzid">
                <param format="mzid" name="psms" type="data" label="MzIdentML containing PSMs" help="select appropriate dataset from history" />
            </when>
            <when value="proteinpilot_peptide_report">
                <param format="tabular" name="psms" type="data" label="ProteinPilot Peptide Report" help="select appropriate dataset from history" />
            </when>
            <when value="tpp_derived_report">
                <param format="tabular" name="psms" type="data" label="Trans-Proteomic Pipeline Derived Peptide Report" help="select appropriate dataset from history" />
                <param name="scan_source_column" label="Peak List Column" type="data_column" data_ref="psms" />
                <param name="scan_id_column" label="Scan ID Column" type="data_column" data_ref="psms" />
                <param name="peptide_column" label="Peptide Column" type="data_column" data_ref="psms" />
            </when>
        </conditional>
        <param format="mzml" name="peak_lists" type="data" label="Peak list (mzML)" multiple="true" help="select MZML dataset of experimental MS/MS scans" />
        <param name="output_type" type="select" label="Output Type" help="Tabular is a spreadsheet containing columns of selected properties listed below. (select tabular as the output type and Peptide sequence as the column type. HTML provides visualization of matches (select HTML as the output type and ProtVis Link as the column type)">
            <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" help="error of fragment ion (in Da). Recommended: 0.5 for LTQ/Orbitrap instrument; 0.01 for HCD/Orbitrap acquisition" />
        <param name="mass_type" type="select" label="Mass Type" help="Monoisotopic: selects most abundant isotopic MS peak for theoretical mass calculation. Average: uses average mass values for theoretical mass calculation. Average mass type is not well supported in this tool">
            <option value="monoisotopic" selected="true">Monoisotopic</option>
            <option value="average">Average (has known problems)</option>
        </param>
        <repeat name="columns" title="Column">
            <conditional name="column">

            <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>
                    <option value="mz_range_absolute">m/z Range (absolute)</option>
                    <option value="mz_range_percent_bp">m/z Range (percent of base peak m/z)</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>
                <when value="mz_range_absolute">
                    <param name="min" label="Minimum m/z" type="float" help="" value="0.0" />
                    <param name="max" label="Maximum m/z" type="float" help="" value="100000.0" />
                </when>
                <when value="mz_range_percent_bp">
                    <param name="min" label="Minimum m/z (as percent of base peak m/z)" type="float" help="" value="0.0" />
                    <param name="max" label="Maximum m/z (as percent of base peak m/z)" type="float" help="" value="100000.0" />
                </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>
    <help>
**What it does**

Generates user-selected metrics in a tabular format for peptide-spectral matches using spectral/peptide summary generated from a search tool and mzml input files. The tabular format that is generated can be used for filtering based on user-defined thresholds. Alternatively, it can also provide visualization of peptide-spectral matches, thus allowing further metrics evaluation.
</help>
</tool>