--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/psm_eval.xml	Fri May 10 18:11:25 2013 -0400
@@ -0,0 +1,235 @@
+<?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>