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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pecan commit 21855dec2949420d3bccfd6c9912578e9aacecf0
author jjohnson
date Fri, 25 Aug 2017 14:25:21 -0400
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1 <tool id="pecan" name="PECAN" version="0.1.0">
2 <description>detect peptides directly from DIA Mass Spec</description>
3 <requirements>
4 <requirement type="package" version="0.9.9.3">pecan</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <version_command>pecan --VERSION</version_command>
10 <command><![CDATA[
11 ## ln mzML file
12 #if $isolation.isolationsrc == 'entered':
13 #set $isolationfile = $isolationSheme
14 #else
15 #set $isolationfile = $isolation.isolation_windows
16 #end if
17 #set $outputRoot = 'test'
18 awk 'NF>1 && $1 ~ /^[0-9]+(\.[0-9]*)?$/{print \$1; print \$2; print "$outputRoot"}' $isolationfile |
19 xargs -n3 -P\${GALAXY_SLOTS}
20 pecan
21 #if $backgroundProteome:
22 --backgroundProteome='$backgroundProteome'
23 #end if
24 --bgDecoyNumber=$bgDecoyNumber
25 #if $decoyTag and str($decoyTag):
26 --decoyTag=$decoyTag
27 #end if
28 --ionTypes=$--ionTypes
29 --minElution=$minElution
30 --maxElution=$maxElution
31 --overlap=$advanced_options.overlap
32 #if $advanced_options.ms1.ms1Unit == 'ppm':
33 --ms1Unit=ppm
34 --ms1Tolerance=$advanced_options.ms1.ms1Tolerance
35 #elif $advanced_options.ms1.ms1Unit == 'mz':
36 --ms1Unit=mz
37 --ms1Tolerance=$advanced_options.ms1.ms1Tolerance
38 #end if
39 #if $advanced_options.ms2.ms2Unit == 'ppm':
40 --ms2Unit=ppm
41 --ms2Tolerance=$advanced_options.ms2.ms2Tolerance
42 #elif $advanced_options.ms2.ms2Unit == 'mz':
43 --ms2Unit=mz
44 --ms2Tolerance=$advanced_options.ms2.ms2Tolerance
45 #end if
46 --minCharge=$advanced_options.minCharge
47 --maxCharge=$advanced_options.maxCharge
48 #if $advanced_options.ms2Boundaries.specify == 'specify':
49 --ms2Boundaries="$advanced_options.ms2Boundaries.ms2BoundariesMin,$advanced_options.ms2Boundaries.ms2BoundariesMax"
50 #end if
51 --alpha=$advanced_options.alpha
52 --beta=$advanced_options.beta
53 --idotp=$advanced_options.idotp
54 --topX=$advanced_options.topX
55 #if $advanced_options.fixedMod and str($advanced_options.fixedMod):
56 --fixedMod='$advanced_options.fixedMod'
57 #end if
58 $input $peptides 2>1 > run.log
59 && cat "$outputRoot"*.log > '$log_file'
60 && cat "$outputRoot"*.td.feature | awk 'NR==1{print $0};!/peakCalibratedScore/{print $0}' > '$feature_file'
61 ]]></command>
62
63 <configfiles>
64 <configfile name="isolationSheme">#slurp
65 #import re
66 #if $isolation.isolationsrc == 'entered':
67 #echo $re.sub(r'(\d+[.]\d+)\s+(\d+[.]\d)\s*',r'\1\t\2\n',$isolation.isolation_windows.strip())
68 #end if
69 #slurp</configfile>
70 </configfiles>
71 <inputs>
72 <param name="input" type="data" format="mzml" label="centroided mzML file"/>
73 <param name="sciex" type="boolean" truevalue="--sciex" falsevalue="" checked="false"
74 label="mzML files were generated from AB SCIEX MS Data Converter"/>
75 <param name="peptides" type="data" format="tabular" multiple="true" label="target peptides"/>
76
77 <conditional name="isolation">
78 <param name="isolationsrc" type="select" label="isolation windows">
79 <option value="entered">Enter isolation windows</option>
80 <option value="history">Read isolation windows from a history dataset</option>
81 </param>
82 <when value="entered">
83 <param name="isolation_windows" type="text" area="true" size="20x20" value="" label="isolation windows">
84 <validator type="regex" message="enter pairs of window boudaries, e.g.:400.0 420.0">^(?ms)(\d+[.]\d+\s\d+[.]\d)(\s\d+[.]\d+\s\d+[.]\d)*$</validator>
85 </param>
86 </when>
87 <when value="history">
88 <param name="isolation_windows" type="data" format="tabular" label="isolation windows"/>
89 </when>
90 </conditional>
91
92 <!-- species - default proteomes for (ecoli/yeast/mouse/human) -->
93 <param name="backgroundProteome" type="data" format="tabular" optional="true" label="BackgroundProteome"
94 help="Peptide list file name of background proteome. Recommended if querying for a small number of peptides."/>
95 <param name="bgDecoyNumber" type="integer" value="2000" min="0" label="Number of decoys used for background estimation"
96 optional="True" help="(-n) Default= 2000" />
97 <param name="decoyTag" type="text" value="decoy" optional="true" label="Tag for decoy sequences in the database"/>
98
99 <param name="ionTypes" type="select" label="Fragment ion types" help="suggested HCD: y, reCID: by">
100 <option value="by">by</option>
101 <option value="y">y</option>
102 <option value="b">b</option>
103 </param>
104
105 <param name="minElution" type="integer" value="12" min="1" label="Minimum time in seconds a peptide is expected to elute"
106 optional="True" help="(-m) Default= 12 seconds" />
107 <param name="maxElution" type="integer" value="30" min="1" label="Maximum time in seconds a peptide is expected to elute"
108 optional="True" help="(-x) Default= 30 seconds" />
109
110 <section name="advanced_options" expanded="false" title="Advanced Options">
111 <param name="overlap" type="integer" value="0" min="0" max="100" label="Overlap percentage of isolation window"/>
112 <conditional name="ms1">
113 <param name="ms1Unit" type="select" label="Unit for precursor ion extraction tolerance">
114 <option value="ppm">ppm</option>
115 <option value="mz">mz</option>
116 </param>
117 <when value="ppm">
118 <param name="ms1Tolerance" type="integer" value="10" min="0" label="ms1Tolerance"
119 help="Mass error for precursor ion extracting"/>
120 </when>
121 <when value="mz">
122 <param name="ms1Tolerance" type="float" value="10" min="0" label="ms1Tolerance"
123 help="Mass error for precursor ion extracting"/>
124 </when>
125 </conditional>
126 <conditional name="ms2">
127 <param name="ms2Unit" type="select" label="Unit for fragment ion extraction tolerance">
128 <option value="ppm">ppm</option>
129 <option value="mz">mz</option>
130 </param>
131 <when value="ppm">
132 <param name="ms2Tolerance" type="integer" value="10" min="0" label="ms2Tolerance"
133 help="Mass error for precursor ion extracting"/>
134 </when>
135 <when value="mz">
136 <param name="ms2Tolerance" type="float" value="10" min="0" label="ms2Tolerance"
137 help="Mass error for precursor ion extracting"/>
138 </when>
139 </conditional>
140 <param name="minCharge" type="integer" value="2" min="1" label="Minimum charge state searched"/>
141 <param name="maxCharge" type="integer" value="3" min="1" label="Maximum charge state searched"/>
142 <conditional name="ms2Boundaries">
143 <param name="specify" type="select" label="Unit for fragment ion extraction tolerance">
144 <option value="calculate">Let PECAN calculate MS2 Boundaries</option>
145 <option value="specify">Specify MS2 Boundaries</option>
146 </param>
147 <when value="calculate"/>
148 <when value="specify">
149 <param name="ms2BoundariesMin" type="float" value="" label="Specify the MS2 scan lower m/z limit for the target window"/>
150 <param name="ms2BoundariesMax" type="float" value="" label="Specify the MS2 scan upper m/z limit for the target window"/>
151 </when>
152 </conditional>
153 <param name="alpha" type="float" value="1.8" min="0.0" label="Alpha hyperparameter to set score threshold for cIons" />
154 <param name="beta" type="float" value="0.4" min="0.0" max="1.0" label="Beta hyperparameter to set score threshold for cIons" />
155 <param name="idotp" type="float" value="0.0" min="0.0" label="MS1 idotp threshold used for peak picking" />
156 <param name="topX" type="integer" value="1" min="1" label="Reporting top x peaks per charged peptide"/>
157
158 <param name="fixedMod" type="text" value="" optional="true" label="Fixed modifications in the sample">
159 <help><![CDATA[
160 Fixed modifications in the sample. For example, default C[+57.021] will treat every Cys
161 in the query sequences and background proteome as C[+57.021] while overwriting any
162 specific modifications on individual Cys
163 If multiple fixed modifications are desired use "," to separate each fixedMod tag
164 (e.g. C[+57.021],M[+15.995])
165 ]]></help>
166 <validator type="regex" message="C[+57.021],M[+15.995]">^([A-Z]\[[+-]\d+[.]\d+\](,[A-Z]\[[+-]\d+[.]\d+\])*)*$</validator>
167 <sanitizer sanitize="False"/>
168 </param>
169 </section>
170 <!--
171 verbosity#Verbosity level for file logging (WARNING/INFO/DEBUG) Default=INFO
172 -->
173 </inputs>
174 <outputs>
175 <data name="log_file" format="txt" label="" />
176 <data name="feature_file" format="percin" label="" />
177 </outputs>
178 <help><![CDATA[
179 **PECAN**
180
181 PECAN (PEptide-Centric ANalysis) is a tool for peptide detection directly from DIA data without the need of a spectral library. PECAN takes a list of peptide sequences and query each peptide against the DIA data (in centroid mzML format) and reports the best evidence of detection for each peptide. The PECAN report is designed for Percolator to separate correct from incorrect matches with false discovery rate (FDR) control.
182
183 usage: pecan [-h] [-d DECOYTAG] [--ms1Unit MS1UNIT] [--ms2Unit MS2UNIT]
184 [-p MS1TOLERANCE] [-q MS2TOLERANCE] [-m MINELUTION]
185 [-x MAXELUTION] [-b BACKGROUNDPROTEOME] [-n BGDECOYNUMBER]
186 [-i IDOTP] [-v VERBOSITY] [-t TOPX] [--minCharge MINCHARGE]
187 [--maxCharge MAXCHARGE] [-s IONTYPES] [--overlap OVERLAP]
188 [--SCIEX] [--VERSION] [--ms2Boundaries MS2BOUNDARIES]
189 [--alpha ALPHA] [--beta BETA] [--fixedMod FIXEDMOD]
190 mzMLFileName peptideListFileName isolationStart isolationEnd
191 outputRoot
192
193
194
195 positional arguments:
196 mzMLFileName path to the centroid .mzML file
197 peptideListFileName path to the query peptide list
198 isolationStart precursor m/z of isolation start
199 isolationEnd precursor m/z of isolation end
200 outputRoot name base of the output files
201
202 optional arguments:
203 -h, --help show this help message and exit
204 -d DECOYTAG, --decoyTag DECOYTAG
205 Tag for decoy sequences in the database
206 Default= decoy
207
208 --ms1Unit MS1UNIT Unit (ppm/mz) for precursor ion extraction tolerance
209 Used with -p
210 Default=ppm
211
212 --ms2Unit MS2UNIT Unit (ppm/mz) for fragment ion extraction tolerance
213 Used with -q
214 Default=ppm
215
216 -p MS1TOLERANCE, --ms1Tolerance MS1TOLERANCE
217 Mass error for precursor ion extracting
218 Default=10
219
220 -q MS2TOLERANCE, --ms2Tolerance MS2TOLERANCE
221 Mass error for fragment ion extracting
222 Default=10
223
224 -m MINELUTION, --minElution MINELUTION
225 Minimum time in seconds a peptide is expected to elute
226 Default= 12 seconds
227
228 -x MAXELUTION, --maxElution MAXELUTION
229 Maximum time in seconds a peptide is expected to elute
230 Default= 30 seconds
231
232 -b BACKGROUNDPROTEOME, --backgroundProteome BACKGROUNDPROTEOME
233 Peptide list file name of background proteome
234 Recommended if querying for a small number of peptides
235 Default=None
236
237 -n BGDECOYNUMBER, --bgDecoyNumber BGDECOYNUMBER
238 Number of decoys used for background estimation
239 Default=2000
240
241 -i IDOTP, --idotp IDOTP
242 MS1 idotp threshold used for peak picking
243 Default=0.000000
244
245 -v VERBOSITY, --verbosity VERBOSITY
246 Verbosity level for file logging (WARNING/INFO/DEBUG)
247 Default=INFO
248
249 -t TOPX, --topX TOPX Reporting top x peaks per charged peptide
250 Default=1
251
252 --minCharge MINCHARGE
253 Minimum charge state searched
254 Default=2
255
256 --maxCharge MAXCHARGE
257 Maximum charge state searched
258 Default=3
259
260 -s IONTYPES, --ionTypes IONTYPES
261 == To be added == Fragment ion types (b, y, or by)
262 Default=by
263
264 --overlap OVERLAP Overlap percentage of isolation window
265 Default=0
266
267 --SCIEX Flag if mzML is generated from AB Sciex converter
268 --VERSION Show current PECAN version
269
270 --ms2Boundaries MS2BOUNDARIES
271 Specify the MS2 scan lower and upper m/z limit such as 200,2000 for the target window
272 If not specify pecan will determine it with a function
273
274 --alpha ALPHA Alpha hyperparameter to set score threshold for cIons
275
276 --beta BETA Beta hyperparameter to set cutoff for number of cIons
277
278 --fixedMod FIXEDMOD Fixed modifications in the sample. For example, default C[+57.021] will treat every Cys
279 in the query sequences and background proteome as C[+57.021] while overwriting any
280 specific modifications on individual Cys
281 If multiple fixed modifications are desired use "," to separate each fixedMod tag
282 (e.g. C[+57.021],M[+15.995])
283
284
285 ]]></help>
286 </tool>