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comparison proteomiqon_peptidespectrummatching.xml @ 0:db6faafbf75b draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
author galaxyp
date Thu, 15 Jul 2021 07:11:01 +0000
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1 <tool id="proteomiqon_peptidespectrummatching" name="ProteomIQon PeptideSpectrumMatching" version="@VERSION@" profile="20.05">
2 <description>
3 iterates across all MS/MS scans in an MS run, determines precursor charge states and possible peptide spectrum matches.
4 </description>
5 <macros>
6 <token name="@VERSION@">0.0.7</token>
7 </macros>
8 <requirements>
9 <requirement type="package" version="@VERSION@">proteomiqon-peptidespectrummatching</requirement>
10 </requirements>
11 <command detect_errors="exit_code"><![CDATA[
12 #import re
13 #set basename = $re.sub(r'[^\w ,.\-+]','_',$instrumentOutput.element_identifier)
14 #if $outputParamfile:
15 cat '$paramfile' >> '$out_paramfile' &&
16 #end if
17 ln -s '$instrumentOutput' '${basename}.mzlite' &&
18 ln -s '$out_psm' '${basename}.psm' &&
19 proteomiqon-peptidespectrummatching -i './${basename}.mzlite' -d '$peptideDB' -p '$paramfile' -o ./
20 ]]>
21 </command>
22 <configfiles>
23 <configfile name="paramfile">
24 <![CDATA[
25 {
26 "ChargeStateDeterminationParams": {
27 "ExpectedMinimalCharge": ${ChargeStateDeterminationParams.ExpectedMinimalCharge},
28 "ExpectedMaximumCharge": ${ChargeStateDeterminationParams.ExpectedMaximumCharge},
29 "Width": ${ChargeStateDeterminationParams.Width},
30 "MinIntensity": ${ChargeStateDeterminationParams.MinIntensity},
31 "DeltaMinIntensity": ${ChargeStateDeterminationParams.DeltaMinIntensity},
32 "NrOfRndSpectra": ${ChargeStateDeterminationParams.NrOfRndSpectra}
33 },
34 "LookUpPPM": ${LookUpPPM},
35 "nTerminalSeries": { "Case": "${nTerminalSeries}" },
36 "cTerminalSeries": { "Case": "${cTerminalSeries}" },
37 "Andromeda": {
38 "PMinPMax": {
39 "Item1": ${Andromeda.PMin},
40 "Item2": ${Andromeda.PMax}
41 },
42 "MatchingIonTolerancePPM": ${Andromeda.MatchingIonTolerancePPM}
43 }
44 }
45 ]]>
46 </configfile>
47 </configfiles>
48 <inputs>
49 <param name="instrumentOutput" type="data" format="sqlite" label="Instrument output" help="Specify mass spectrometry data you want to analyze."/>
50 <param name="peptideDB" type="data" format="sqlite" label="Peptide database" help="Specify the peptide data base."/>
51 <section name="ChargeStateDeterminationParams" title="Charge state determination parameters" >
52 <param name="ExpectedMinimalCharge" type="integer" min="1" max="8" value="2" label="Expected minimal charge" help="Specify the minimum peptide ion charge state to consider."/>
53 <param name="ExpectedMaximumCharge" type="integer" min="1" max="8" value="5" label="Expected maximum charge" help="Specify the maximum peptide ion charge state to consider."/>
54 <param name="Width" type="float" value="1.1" label="Width" help="Specify the width around the picked precursor ion used in charge state determination."/>
55 <param name="MinIntensity" type="float" value="0.15" label="Min intensity" help="Specify minimum relative intensity within an putative isotopic envelope to be included when performing charge state determination."/>
56 <param name="DeltaMinIntensity" type="float" value="0.3" label="Delta min intensity" help="Specify minimum relative intensity to the prior peak when iterating through peak lists while performing charge state determination."/>
57 <param name="NrOfRndSpectra" type="integer" value="10000" label="Number of random spectra" help="When performing charge state determination we compared measured envelopes to the distribution of randomly generated spectra. This parameter tunes the size of the generated data set."/>
58 </section>
59 <param name="LookUpPPM" type="float" value="30" label="Lookup PPM" help="Specify the width of the search space when retrieving in silico generated peptide ions from the peptide data base. The width is calculated relative to the precursor mz in ppm."/>
60 <param name="nTerminalSeries" type="select" optional="false" label="N-terminal series" help="Specify the types of N-terminal charged ion fragments included in the generation of in silico fragment spectra." multiple="true" display="checkboxes">
61 <option value="A">A</option>
62 <option value="B" selected="true">B</option>
63 <option value="C">C</option>
64 </param>
65 <param name="cTerminalSeries" type="select" optional="false" label="C-terminal Series" help="Specify the types of C-terminal charged ion fragments included in the generation of in silico fragment spectra." multiple="true" display="checkboxes">
66 <option value="X">X</option>
67 <option value="Y" selected="true">Y</option>
68 <option value="Z">Z</option>
69 </param>
70 <section name="Andromeda" title="Andromeda">
71 <param name="PMin" type="integer" value="4" label="P min" help="Specify the minimum N of the top N most abundand peaks within a 100 Da window used to compute the Andromeda score."/>
72 <param name="PMax" type="integer" value="10" label="P max" help="Specify the maximum N of the top N most abundand peaks within a 100 Da window used to compute the Andromeda score."/>
73 <param name="MatchingIonTolerancePPM" type="float" value="100.0" label="Matching ion tolerance PPM" help="Specify the minimum m/z difference between a measured and an in silico generated peak during peak matching. The width is calculated relative to the m/z of the measured peak in ppm."/>
74 </section>
75 <param name="outputParamfile" type="boolean" value="false" label="Output parameter file"/>
76 </inputs>
77 <outputs>
78 <data format="tabular" name="out_psm" />
79 <data format="json" name="out_paramfile">
80 <filter>outputParamfile</filter>
81 </data>
82 </outputs>
83 <tests>
84 <test expect_num_outputs="1">
85 <param name="instrumentOutput" value="sample.mzlite"/>
86 <param name="peptideDB" value="sample.db"/>
87 <param name="LookUpPPM" value="30"/>
88 <param name="nTerminalSeries" value="A"/>
89 <param name="cTerminalSeries" value="X"/>
90 <section name="ChargeStateDeterminationParams">
91 <param name="ExpectedMinimalCharge" value="2"/>
92 <param name="ExpectedMaximumCharge" value="5"/>
93 <param name="Width" value="1.1"/>
94 <param name="MinIntensity" value="0.15"/>
95 <param name="DeltaMinIntensity" value="0.3"/>
96 <param name="NrOfRndSpectra" value="10000"/>
97 </section>
98 <section name="Andromeda">
99 <param name="PMin" value="4"/>
100 <param name="PMax" value="10"/>
101 <param name="MatchingIonTolerancePPM" value="100.0"/>
102 </section>
103 <param name="outputParamfile" value="false"/>
104 </test>
105 <test expect_num_outputs="2">
106 <param name="instrumentOutput" value="sample.mzlite"/>
107 <param name="peptideDB" value="sample.db"/>
108 <param name="LookUpPPM" value="30"/>
109 <param name="nTerminalSeries" value="B"/>
110 <param name="cTerminalSeries" value="Y"/>
111 <section name="ChargeStateDeterminationParams">
112 <param name="ExpectedMinimalCharge" value="2"/>
113 <param name="ExpectedMaximumCharge" value="5"/>
114 <param name="Width" value="1.1"/>
115 <param name="MinIntensity" value="0.15"/>
116 <param name="DeltaMinIntensity" value="0.3"/>
117 <param name="NrOfRndSpectra" value="10000"/>
118 </section>
119 <section name="Andromeda">
120 <param name="PMin" value="4"/>
121 <param name="PMax" value="10"/>
122 <param name="MatchingIonTolerancePPM" value="100.0"/>
123 </section>
124 <param name="outputParamfile" value="true"/>
125 <output name="out_paramfile" file="result_1.json"/>
126 </test>
127 <test expect_num_outputs="2">
128 <param name="instrumentOutput" value="sample.mzlite"/>
129 <param name="peptideDB" value="sample.db"/>
130 <param name="LookUpPPM" value="30"/>
131 <param name="nTerminalSeries" value="A"/>
132 <param name="cTerminalSeries" value="Z"/>
133 <section name="ChargeStateDeterminationParams">
134 <param name="ExpectedMinimalCharge" value="2"/>
135 <param name="ExpectedMaximumCharge" value="5"/>
136 <param name="Width" value="1.1"/>
137 <param name="MinIntensity" value="0.15"/>
138 <param name="DeltaMinIntensity" value="0.3"/>
139 <param name="NrOfRndSpectra" value="10000"/>
140 </section>
141 <section name="Andromeda">
142 <param name="PMin" value="4"/>
143 <param name="PMax" value="10"/>
144 <param name="MatchingIonTolerancePPM" value="100.0"/>
145 </section>
146 <param name="outputParamfile" value="true"/>
147 <output name="out_paramfile" file="result_2.json"/>
148 </test>
149 <test expect_num_outputs="2">
150 <param name="instrumentOutput" value="sample.mzlite"/>
151 <param name="peptideDB" value="sample.db"/>
152 <param name="LookUpPPM" value="30"/>
153 <param name="nTerminalSeries" value="C"/>
154 <param name="cTerminalSeries" value="X"/>
155 <section name="ChargeStateDeterminationParams">
156 <param name="ExpectedMinimalCharge" value="2"/>
157 <param name="ExpectedMaximumCharge" value="5"/>
158 <param name="Width" value="1.1"/>
159 <param name="MinIntensity" value="0.15"/>
160 <param name="DeltaMinIntensity" value="0.3"/>
161 <param name="NrOfRndSpectra" value="10000"/>
162 </section>
163 <section name="Andromeda">
164 <param name="PMin" value="4"/>
165 <param name="PMax" value="10"/>
166 <param name="MatchingIonTolerancePPM" value="100.0"/>
167 </section>
168 <param name="outputParamfile" value="true"/>
169 <output name="out_paramfile" file="result_3.json"/>
170 </test>
171 </tests>
172 <help>
173 <![CDATA[
174 What It Does
175 ------------
176 **Disclaimer** this tool needs a peptide database to query against, if you did not create one yet you can do so by using the `PeptideDB <https://csbiology.github.io/ProteomIQon/tools/PeptideDB.html>`_ tool.
177
178 Given raw a MS run in the mzite format, this tool iterates accross all recorded MS/MS scans and determines the charge state of precursor ions which were selected for fragmentation.
179 With this it is possible to query the peptide data base for every precursor ion mass +/- a tolerance (which defines the so called 'search space') and retrieve peptides that are
180 theoretical candidates for a match. For each of the peptide candidates we create an theoretical spectrum in silico and compare it to the measured MS/MS scan.
181
182 .. image:: PSM.png
183 :width: 768pt
184 :height: 563pt
185
186 To measure similarity we use our own implementations of three established search enginge scores: SEQUEST, Andromeda and XTandem.
187 The search space is extended by so called decoys. Decoys are reversed counterparts of peptides within the search space and allow
188 us to assign a false discovery rate to each scored peptide using the `PSMStatistics <https://csbiology.github.io/ProteomIQon/tools/PSMStatistics.html>`_ tool.
189
190 Further Reading
191 ---------------
192 Additional information about the tool can be found in the `documentation <https://csbiology.github.io/ProteomIQon/tools/PeptideSpectrumMatching.html>`_.
193 ]]>
194 </help>
195 </tool>