Mercurial > repos > galaxyp > proteomiqon_peptidespectrummatching
comparison proteomiqon_peptidespectrummatching.xml @ 0:db6faafbf75b draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteomiqon_peptidespectrummatching commit 2ae9320c0e55f3a2a7d5b6121002722e59b42ab4"
author | galaxyp |
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date | Thu, 15 Jul 2021 07:11:01 +0000 |
parents | |
children | a79a24eb9e76 |
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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> |