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comparison psm_eval.xml @ 0:77cc9cc99e15 draft

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Initial commit.
author galaxyp
date Fri, 10 May 2013 18:11:25 -0400
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1 <?xml version="1.0"?>
2 <tool name="Peptide-Spectrum-Matches (PSMs) Evaluation" id="psm_eval" version="0.1.0">
3 <requirements>
4 <requirement type="package">psm_eval</requirement>
5 </requirements>
6 <description>Re-evalute potential PSMs using the psm-eval application.</description>
7 <command>psm_eval --settings $driver</command>
8 <configfiles>
9 <configfile name="driver"># YAML driver for PSM Eval
10 peak_lists:
11 #for $peak_list in $peak_lists:
12 - path: $peak_list
13 name: "$peak_list.display_name"
14 encoded_id: "${$__app__.security.encode_id( $peak_list.id )}"
15 #end for
16 psms: $psms_cond.psms
17 psms_type: $psms_cond.type
18 output: $output
19 output_format: $output_type
20 mass_type: $mass_type
21 mass_tolerance: $default_mass_tolerance
22 columns:
23 #for $column in $columns
24 #set $column_options = $column.column
25 #set $type = str(column_options['type'])
26 - type: ${type}
27 #if $type in ['ions_matched', 'peaks_matched']
28 aggregate_by: $column_options.aggregate_by
29 #if $column_options.tolerance.specify
30 mass_tolerance: $column_options.tolerance.tolerance
31 #end if
32 #end if
33 #if $type in ['ions_matched', 'peaks_matched', 'num_peaks']
34 ## Handle peak filters
35 peak_filters:
36 #for $peak_filter in $column_options.peak_filters
37 #set $peak_filter_options = $peak_filter.peak_filter
38 #set $peak_filter_type = str(peak_filter_options['peak_filter_type'])
39 - type: $peak_filter_type
40 #if $peak_filter_type in ['percent_tic', 'quantile', 'percent_max_intensity']
41 percent: $peak_filter_options.percent
42 #end if
43 #if $peak_filter_type == 'quantile'
44 q: $peak_filter_options.q
45 k: $peak_filter_options.k
46 #end if
47 #end for
48 #end if
49 #if $type in ['ions_matched', 'peaks_matched']
50 ## Handle ions series
51 #set $ions = $column_options
52 ions:
53 series: $ions.ion_series
54 #if $ions.losses
55 losses: $ions.losses
56 #end if
57 #end if
58 #if $type == "source_statistic"
59 statistic_name: ${str(column_options['source_statistic'])}
60 #end if
61 #if $type == "link"
62 link_type: galaxy
63 #end if
64 #end for
65 </configfile>
66 </configfiles>
67 <inputs>
68 <conditional name="psms_cond">
69 <param name="type" type="select" label="PSMs Type" help="">
70 <option value="mzid">MzIdentML (mzid)</option>
71 <option value="proteinpilot_peptide_report">ProteinPilot Peptide Report</option>
72 </param>
73 <when value="mzid">
74 <param format="mzid" name="psms" type="data" label="MzIdentML containing PSMs" help="" />
75 </when>
76 <when value="proteinpilot_peptide_report">
77 <param format="tabular" name="psms" type="data" label="ProteinPilot Peptide Report" help="" />
78 </when>
79 </conditional>
80 <param format="mzml" name="peak_lists" type="data" label="Peak list (mzML)" multiple="true" help="" />
81 <param name="output_type" type="select" label="Output Type" help="">
82 <option value="tsv">Tabular (tsv)</option>
83 <option value="html">HTML</option>
84 </param>
85 <param name="default_mass_tolerance" type="float" label="Default Mass Tolerance" value="0.5" />
86 <param name="mass_type" type="select" label="Mass Type">
87 <option value="monoisotopic" selected="true">Monoisotopic</option>
88 <option value="average">Average (has known problems)</option>
89 </param>
90 <repeat name="columns" title="Column">
91 <conditional name="column">
92 <param type="select" name="type" label="Column Type">
93 <option value="peptide">Peptide Sequence</option>
94 <option value="scan_index">Scan Index</option>
95 <option value="scan_number">Scan Number</option>
96 <option value="scan_id">Scan ID</option>
97 <option value="scan_source">Peak List</option>
98 <option value="num_peaks">Number of Peaks</option>
99 <option value="peaks_matched">Peaks Matched Statistic</option>
100 <option value="ions_matched">Ions Matched Statistic</option>
101 <option value="total_ion_current">Total Ion Current</option>
102 <option value="source_statistic">Statistic from PSM Source</option>
103 <option value="link">ProtVis Link</option>
104 </param>
105 <when value="num_peaks">
106 <expand macro="peak_filters" />
107 </when>
108 <when value="peaks_matched">
109 <param name="aggregate_by" label="Peak Matching Statistic" type="select">
110 <option value="count">Number of Matched Peaks</option>
111 <option value="count_missed">Number of Unmatched Peaks</option>
112 <option value="percent">Percent of Matched Peaks</option>
113 <option value="percent_missed">Percent of Unmatched Peaks</option>
114 </param>
115 <expand macro="ions" />
116 <expand macro="peak_filters" />
117 <expand macro="tolerance_conditional" />
118 </when>
119 <when value="ions_matched">
120 <param name="aggregate_by" label="Ion Matching Statistic" type="select">
121 <option value="count">Number of Matched Ions</option>
122 <option value="count_missed">Number of Unmatched Ions</option>
123 <option value="count_longest_stretch">Longest Stretch of Matched Ions</option>
124 <option value="percent">Percent of Matched Ions</option>
125 <option value="percent_missed">Percent of Unmatched Ions</option>
126 <option value="list_matches">List Matched Ions</option>
127 <option value="list_misses">List Unmatched Ions</option>
128 </param>
129 <expand macro="ions" />
130 <expand macro="peak_filters" />
131 <expand macro="tolerance_conditional" />
132 </when>
133 <when value="source_statistic">
134 <param name="source_statistic" label="PSM Source Statistic" type="select">
135 <option value="xcorr">xcorr</option>
136 <option value="MyriMatch:MVH">MyriMatch: MVH</option>
137 <option value="MyriMatch:mzFidelity">MyriMatch: mzFidelity</option>
138 <option value="Conf">Conf</option>
139 </param>
140 </when>
141 <when value="link">
142 </when>
143 </conditional>
144 </repeat>
145 </inputs>
146 <outputs>
147 <data format="tabular" name="output" label="PSM Evaluation of ${on_string}">
148 <change_format>
149 <when input="output_type" value="html" format="html" />
150 </change_format>
151 </data>
152 </outputs>
153 <macros>
154 <macro name="ions">
155 <param name="ion_series" type="select" multiple="true" label="Ion Series">
156 <option value="a1">a1</option>
157 <option value="a2">a2</option>
158 <option value="a3">a3</option>
159 <option value="b1">b1</option>
160 <option value="b2">b2</option>
161 <option value="b3">b3</option>
162 <option value="c1">c1</option>
163 <option value="c2">c2</option>
164 <option value="c3">c3</option>
165 <option value="x1">x1</option>
166 <option value="x2">x2</option>
167 <option value="x3">x3</option>
168 <option value="y1">y1</option>
169 <option value="y2">y2</option>
170 <option value="y3">y3</option>
171 <option value="z1">z1</option>
172 <option value="z2">z2</option>
173 <option value="z3">z3</option>
174 <option value="m1">M1</option>
175 <option value="m2">M2</option>
176 <option value="internal">Internal Ions</option>
177 </param>
178 <param name="losses" type="select" multiple="true" label="Losses" value="">
179 <option value="H2O">H2O</option>
180 <option value="NH3">NH3</option>
181 <option value="CO">CO (-28) on internal ions</option>
182 </param>
183 </macro>
184 <macro name="tolerance_conditional">
185 <conditional name="tolerance">
186 <param name="specify" label="Specify Mass Tolerance" type="boolean" />
187 <when value="false">
188 </when>
189 <when value="true">
190 <param name="tolerance" value="0.5" label="Tolerance" type="float" />
191 </when>
192 </conditional>
193 </macro>
194 <!--
195 <macro name="conditional_ions">
196 <conditional name="specify_ions">
197 <param type="boolean" truevalue="true" falsevalue="false" name="specify" label="Specify Ions?" />
198 <when value="true">
199 <expand macro="ions" />
200 </when>
201 <when value="false" />
202 </conditional>
203 </macro>
204 -->
205 <macro name="peak_filters">
206 <repeat name="peak_filters" title="Peak Filter">
207 <expand macro="peak_filter" />
208 </repeat>
209 </macro>
210 <macro name="peak_filter">
211 <conditional name="peak_filter">
212 <param type="select" label="Filter Peaks on" name="peak_filter_type">
213 <option value="percent_tic">Intensity as a Percent of Total Ion Current</option>
214 <option value="quantile">Intensity Quantile</option>
215 <option value="percent_max_intensity">Intensity as a Percent of Maximum Spectrum Peak Intensity</option>
216 </param>
217 <when value="percent_tic">
218 <expand macro="percent_param" />
219 </when>
220 <when value="percent_max_intensity">
221 <param name="percent" label="Percent of Maximum Peak Intensity" type="float" value="0.1" />
222 </when>
223 <when value="quantile">
224 <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" />
225 <param name="k" label="k" type="integer" value="1"/>
226 <expand macro="percent_param" />
227 </when>
228 </conditional>
229 <!-- TODO: Add m/z, intensity thresholds. -->
230 </macro>
231 <macro name="percent_param">
232 <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" />
233 </macro>
234 </macros>
235 </tool>