Mercurial > repos > pieterlukasse > prims_masscomb
comparison masscomb_dbsearch_xtandem.xml @ 0:d6001e8d7441
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author | pieter.lukasse@wur.nl |
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date | Wed, 08 Jan 2014 11:34:51 +0100 |
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children | b34fb7461546 |
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1 <tool name="X!Tandem" id="masscomb_xtandem200" version="2.0.0"> | |
2 <description>MS/MS DB search</description> | |
3 <!-- | |
4 For remote debugging start you listener on port 8000 and use the following as command interpreter: | |
5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 | |
6 --> | |
7 <command interpreter="java -jar"> | |
8 MassComb.jar | |
9 -action XTANDEMSEARCH | |
10 -outputFile $outputFile | |
11 -fileGrouping $fileType.type | |
12 -inputFile $fileType.inputFile | |
13 -parametersFile $parametersFile | |
14 -outputTsv $outTsv | |
15 -outReport $htmlReportFile | |
16 -outReportPicturesPath $htmlReportFile.files_path | |
17 </command> | |
18 <inputs> | |
19 <conditional name="fileType"> | |
20 <param name="type" type="select" label="select MS/MS input type"> | |
21 <option value="single" selected="true">single-File</option> | |
22 <option value="fileSet">fileSet</option> | |
23 </param> | |
24 <when value="single"> | |
25 <param name="inputFile" type="data" format="mzml" label="MS/MS input file (mzml)"/> | |
26 </when> | |
27 <when value="fileSet"> | |
28 <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/> | |
29 </when> | |
30 </conditional> | |
31 | |
32 <param name="precursor_mass_tolerance_lower" type="text" size="30" label="precursor monoisotopic mass_tolerance_lower" value="100" help=""/> | |
33 <param name="precursor_mass_tolerance_upper" type="text" size="30" label="precursor monoisotopic mass_tolerance_upper" value="100" help=""/> | |
34 <param name="precursor_error_units" type="select" label="precursor_error_units" help=""> | |
35 <option value="ppm" selected="true">ppm</option> | |
36 <option value="Daltons">Daltons</option> | |
37 </param> | |
38 <param name="fragment_mass_tolerance" type="text" size="30" label="fragment_mass_tolerance" value="0.4" help=""/> | |
39 <param name="fragment_error_units" type="select" label="fragment_error_units" help=""> | |
40 <option value="ppm">ppm</option> | |
41 <option value="Daltons" selected="true">Daltons</option> | |
42 </param> | |
43 <param name="database" type="data" format="fasta" label="Protein sequences DB (FASTA)"/> | |
44 <!-- | |
45 <param name="min_precursor_charge" type="text" size="30" label="min_precursor_charge" value="1" help=""/> | |
46 <param name="max_precursor_charge" type="text" size="30" label="max_precursor_charge" value="4" help=""/>--> | |
47 <param name="fixed_modifications" type="select" display="checkboxes" multiple="true" label="Complete modifications" help=""> | |
48 <option value="57.021464@C">Carbamidomethyl (C)</option> | |
49 <option value="57.021464@C,10.008269@R,8.014199@K">Cam+SILAC (8@K,10@R)</option> | |
50 <option value="57.021464@C,4.025107@K,6.020129@R">Cam+SILAC (4@K,6@R)</option> | |
51 <option value="57.021464@C,4.025107@K,6.020129@R,6.020129@L">Cam+SILAC (4@K,6@R,6@L)</option> | |
52 <option value="58.005479@C">Carboxymethyl (C)</option> | |
53 <option value="45.987721@C">Methylthio (C)</option> | |
54 <option value="47.984744@C">Trioxidation (C)</option> | |
55 <option value="442.224991@C">ICAT-D (C)</option> | |
56 <option value="450.275205@C">ICAT-D:2H(8) (C)</option> | |
57 <option value="227.126991@C">ICAT-C (C)</option> | |
58 <option value="236.157185@C">ICAT-C:13C(9) (C)</option> | |
59 <option value="58.005479@C">Carboxymethyl (C)</option> | |
60 <option value="105.057849@C">Pyridylethyl (C)</option> | |
61 <option value="71.037114@C">Propionamide (C)</option> | |
62 <option value="125.047679@C">Nethylmaleimide (C)</option> | |
63 <option value="144.102063@[,144.102063@K">iTRAQ (N-term,K)</option> | |
64 <option value="57.021464@C,144.102063@[,144.102063@K">Cam + iTRAQ (C,N-term,K)</option> | |
65 <option value="57.021464@C,224.152478@K,224.152478@[">Cam + TMT (C,K,nt)</option> | |
66 <option value="57.021464@C,225.155833@K,225.155833@[">Cam + TMT2plex (C,K,nt)</option> | |
67 <option value="57.021464@C,229.1629328@K,229.1629328@[">Cam + TMT6plex (C,K,nt)</option> | |
68 <option value="57.021464@C,28.0313@[,28.0313@K">Cam + Dimethyl (C,28@N-term,K)</option> | |
69 <option value="57.021464@C,32.0564@[,32.0564@K">Cam + Dimethyl (C,32@N-term,K)</option> | |
70 <option value="57.021464@C,36.0757@[,36.0757@K">Cam + Dimethyl (C,36@N-term,K)</option> | |
71 <option value="45.987721@C,144.102063@[,144.102063@K">Methylthio + iTRAQ (C,N-term,K)</option> | |
72 <option value="45.987721@C,224.152478@K,224.152478@[">Methylthio + TMT (C,K,nt)</option> | |
73 <option value="45.987721@C,225.155833@K,225.155833@[">Methylthio + TMT2plex (C,K,nt)</option> | |
74 <option value="45.987721@C,229.1629328@K,229.1629328@[">Methylthio + TMT6plex (C,K,nt)</option> | |
75 <option value="14.0156@],14.0156@D,14.0156@E">Methy +14Da (D,E,C-term)</option> | |
76 </param> | |
77 <param name="potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications" help=""> | |
78 <option value="15.994915@M">Oxidation (M)</option> | |
79 <option value="15.994915@W">Oxidation (W)</option> | |
80 <option value="0.984016@N">Deamidation (N)</option> | |
81 <option value="0.984016@Q">Deamidation (Q)</option> | |
82 <option value="79.966331@S">Phospho (S)</option> | |
83 <option value="79.966331@T">Phospho (T)</option> | |
84 <option value="79.966331@Y">Phospho (Y)</option> | |
85 <option value="79.956815@Y">Sulfo (Y)</option> | |
86 <option value="42.010565@K">Acetyl (K)</option> | |
87 <option value="43.005814@[">Carbamyl (nt)</option> | |
88 <option value="43.005814@K">Carbamyl (K)</option> | |
89 <option value="72.021129@[">Carboxyethyl (nt)</option> | |
90 <option value="72.021129@K">Carboxyethyl (K)</option> | |
91 <option value="57.021464@[">Carbamidomethyl (nt)</option> | |
92 <option value="57.021464@K">Carbamidomethyl (K)</option> | |
93 <option value="57.021464@C">Carbamidomethyl (C)</option> | |
94 <option value="58.005479@C">Carboxymethyl (C)</option> | |
95 <option value="45.987721@C">Methylthio (C)</option> | |
96 <option value="125.047679@C">Nethylmaleimide (C)</option> | |
97 <option value="31.989829@C">Dioxidation (C)</option> | |
98 <option value="47.984744@C">Trioxidation (C)</option> | |
99 <option value="27.994915@K">formyl (K)</option> | |
100 <option value="27.994915@[">formyl (nt)</option> | |
101 <option value="114.042927@K">GlyGly (K)</option> | |
102 <option value="8.0502@C">ICAT-D:2H(8) (C)</option> | |
103 <option value="9.0302@C">ICAT-C:13C(9) (C)</option> | |
104 <option value="144.102063@[">iTRAQ (N-term)</option> | |
105 <option value="144.102063@K">iTRAQ (K)</option> | |
106 <option value="6.020129@L">Label:13C(6) (L)</option> | |
107 <option value="6.020129@K">Label:13C(6) (K)</option> | |
108 <option value="8.014199@K">Label:13C(6)15N(2) (K)</option> | |
109 <option value="6.020129@R">Label:13C(6) (R)</option> | |
110 <option value="4.025107@K">Label:2H(4) (K)</option> | |
111 <option value="125.047679@C">Nethylmaleimide (C)</option> | |
112 <option value="31.005814@C">Sulfinamide (C)</option> | |
113 <option value="224.152478@K,224.152478@[">TMT (K,nt)</option> | |
114 <option value="225.155833@K,225.155833@[">TMT2plex (K,nt)</option> | |
115 <option value="229.1629328@K,229.1629328@[">TMT6plex (K,nt)</option> | |
116 </param> | |
117 <!-- | |
118 <param name="missed_cleavages" type="text" size="30" label="missed_cleavages" value="1" help="Nr. of possible cleavage sites missed by the enzyme"/>--> | |
119 <param name="minimum_fragment_mz" type="text" size="30" label="minimum_fragment_mz" value="150" help=""/> | |
120 <param name="cleavage_site" type="select" label="cleavage_site" help=""> | |
121 <option selected="true" value="[RK]|{P}">trypsin, [RK]|{P}</option> | |
122 <option value="[R]|[X]">endo-arg-C, [R]|[X]</option> | |
123 <option value="[K]|[X]">endo-lys-C, [K]|[X]</option> | |
124 <option value="[E]|[X]">endo-glu-C, [E]|[X]</option> | |
125 <option value="[X]|[D]">endo-asp-N, [X]|[D]</option> | |
126 <option value="[ED]|[X]">V8, [ED]|[X]</option> | |
127 <option value="[FYWL]|{P}">chymotrypsin, [FYWL]|{P}</option> | |
128 </param> | |
129 <param name="maximum_missed_cleavage_sites" type="integer" size="10" value="1" | |
130 label="maximum missed cleavage sites" | |
131 help="maximum number of missed cleavage sites allowed within a peptide. For a specific, | |
132 aggressive enzyme such as trypsin, the number of missed sites will be low: a value of 1 or 2 is appropriate. | |
133 For a non-specific enzyme, such as pepsin, then a value of 50 is more appropriate."/> | |
134 <param name="max_valid_expect" type="text" size="30" label="maximum valid expectation value" value="0.1" | |
135 help="Max E-Value of a hit to be reported. All results with expectation values less than this value | |
136 are considered to be statisitically significant and are recorded. "/> | |
137 <conditional name="refinementOpt"> | |
138 <param name="refinement" type="select" label="Refine search" help="Select this to enable a second round of more | |
139 detailed searching, using only the set of proteins found by the contraints above. E.g. | |
140 Rather than entering the 'potential modifications' in the options above, try entering them here only. This is | |
141 faster and limits this more thorough searching to a set of proteins for which there is already some evidence."> | |
142 <option value="yes">Yes</option> | |
143 <option value="no" selected="true">No</option> | |
144 </param> | |
145 <when value="yes"> | |
146 <param name="refine_point_mutation" type="select" label="Allow for point mutations (substitutions)" | |
147 help="Test the selected sequences for the possibility of a point mutation in each one of the | |
148 peptides generated with the initial cleavage chemistry."> | |
149 <option value="yes" selected="true">Yes</option> | |
150 <option value="no">No</option> | |
151 </param> | |
152 <param name="refine_potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications to look for in refined search" help=""> | |
153 <option value="15.994915@M">Oxidation (M)</option> | |
154 <option value="15.994915@W">Oxidation (W)</option> | |
155 <option value="0.984016@N">Deamidation (N)</option> | |
156 <option value="0.984016@Q">Deamidation (Q)</option> | |
157 <option value="79.966331@S">Phospho (S)</option> | |
158 <option value="79.966331@T">Phospho (T)</option> | |
159 <option value="79.966331@Y">Phospho (Y)</option> | |
160 <option value="79.956815@Y">Sulfo (Y)</option> | |
161 <option value="42.010565@K">Acetyl (K)</option> | |
162 <option value="43.005814@[">Carbamyl (nt)</option> | |
163 <option value="43.005814@K">Carbamyl (K)</option> | |
164 <option value="72.021129@[">Carboxyethyl (nt)</option> | |
165 <option value="72.021129@K">Carboxyethyl (K)</option> | |
166 <option value="57.021464@[">Carbamidomethyl (nt)</option> | |
167 <option value="57.021464@K">Carbamidomethyl (K)</option> | |
168 <option value="57.021464@C">Carbamidomethyl (C)</option> | |
169 <option value="58.005479@C">Carboxymethyl (C)</option> | |
170 <option value="45.987721@C">Methylthio (C)</option> | |
171 <option value="125.047679@C">Nethylmaleimide (C)</option> | |
172 <option value="31.989829@C">Dioxidation (C)</option> | |
173 <option value="47.984744@C">Trioxidation (C)</option> | |
174 <option value="27.994915@K">formyl (K)</option> | |
175 <option value="27.994915@[">formyl (nt)</option> | |
176 <option value="114.042927@K">GlyGly (K)</option> | |
177 <option value="8.0502@C">ICAT-D:2H(8) (C)</option> | |
178 <option value="9.0302@C">ICAT-C:13C(9) (C)</option> | |
179 <option value="144.102063@[">iTRAQ (N-term)</option> | |
180 <option value="144.102063@K">iTRAQ (K)</option> | |
181 <option value="6.020129@L">Label:13C(6) (L)</option> | |
182 <option value="6.020129@K">Label:13C(6) (K)</option> | |
183 <option value="8.014199@K">Label:13C(6)15N(2) (K)</option> | |
184 <option value="6.020129@R">Label:13C(6) (R)</option> | |
185 <option value="4.025107@K">Label:2H(4) (K)</option> | |
186 <option value="125.047679@C">Nethylmaleimide (C)</option> | |
187 <option value="31.005814@C">Sulfinamide (C)</option> | |
188 <option value="224.152478@K,224.152478@[">TMT (K,nt)</option> | |
189 <option value="225.155833@K,225.155833@[">TMT2plex (K,nt)</option> | |
190 <option value="229.1629328@K,229.1629328@[">TMT6plex (K,nt)</option> | |
191 </param> | |
192 <param name="refine_max_valid_expect" type="text" size="30" label="maximum valid expectation value for identifications coming from refine step" value="0.01" | |
193 help="Max E-Value of a 'refine based' hit to be reported. Notice that the default value here is stricter than | |
194 the same parameter for 'non-refine based' identifications above. "/> | |
195 </when> | |
196 </conditional> | |
197 <param name="reverse_scoring" type="select" label="Scoring, include reverse" help=" Use the X! Tandem protein sequence reverse method (sequences are reversed in memory and searched again, the tag ':reversed' is added to the protein description)."> | |
198 <option value="yes">Yes</option> | |
199 <option value="no" selected="true">No</option> | |
200 <option value="only">Only</option> | |
201 </param> | |
202 | |
203 </inputs> | |
204 <configfiles> | |
205 <configfile name="parametersFile"><?xml version="1.0" encoding="UTF-8"?> | |
206 <tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper"> | |
207 <Files/> | |
208 <Parameters> | |
209 <Attribute attributeName="xtandemLocation" value="/home/lukas007/galaxy-dist/tool-data/prims/tandem-linux-12-10-01-1/bin/" type="Unknown" description=""/> | |
210 <Attribute attributeName="database" value="${database}" type="Unknown" description=""/> | |
211 <Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/> | |
212 <Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/> | |
213 <Attribute attributeName="precursor_error_units" toolSpecificName="spectrum, parent monoisotopic mass error units" value="${precursor_error_units}" type="Unknown" description=""/> | |
214 <Attribute attributeName="fragment_mass_tolerance" toolSpecificName="spectrum, fragment monoisotopic mass error" value="${fragment_mass_tolerance}" type="Unknown" description=""/> | |
215 <Attribute attributeName="fragment_error_units" toolSpecificName="spectrum, fragment monoisotopic mass error units" value="${fragment_error_units}" type="Unknown" description=""/> | |
216 <Attribute attributeName="fixed_modifications" toolSpecificName="residue, modification mass" value="${fixed_modifications}" type="Unknown" description=""/> | |
217 <Attribute attributeName="potential_modifications" toolSpecificName="residue, potential modification mass" value="${potential_modifications}" type="Unknown" description=""/> | |
218 <Attribute attributeName="minimum_fragment_mz" toolSpecificName="spectrum, minimum fragment mz" value="${minimum_fragment_mz}" type="Unknown" description=""/> | |
219 <Attribute attributeName="cleavage_site" toolSpecificName="protein, cleavage site" value="${cleavage_site}" type="Unknown" description=""/> | |
220 <Attribute attributeName="maximum_missed_cleavage_sites" toolSpecificName="scoring, maximum missed cleavage sites" value="${maximum_missed_cleavage_sites}" type="Unknown" description=""/> | |
221 <Attribute attributeName="max_valid_expect" toolSpecificName="output, maximum valid expectation value" value="${max_valid_expect}" type="Unknown" description=""/> | |
222 <Attribute attributeName="refinement" toolSpecificName="refine" value="${refinementOpt.refinement}" type="Unknown" description=""/> | |
223 #if $refinementOpt.refinement == "yes" | |
224 <Attribute attributeName="refine_point_mutation" toolSpecificName="refine, point mutations" value="${refinementOpt.refine_point_mutation}" type="Unknown" description=""/> | |
225 <Attribute attributeName="refine_potential_modifications" toolSpecificName="refine, potential modification mass" value="${refinementOpt.refine_potential_modifications}" type="Unknown" description=""/> | |
226 <Attribute attributeName="refine_max_valid_expect" toolSpecificName="refine, maximum valid expectation value" value="${refinementOpt.refine_max_valid_expect}" type="Unknown" description=""/> | |
227 #end if | |
228 <Attribute attributeName="reverse_scoring" toolSpecificName="scoring, include reverse" value="${reverse_scoring}" type="Unknown" description=""/> | |
229 </Parameters> | |
230 </tns:Program> | |
231 </configfile> | |
232 </configfiles> | |
233 <outputs> | |
234 <data name="outputFile" format="bioml" label="${tool.name} on ${on_string} - Results XML"> | |
235 <change_format> | |
236 <when input="fileType.type" value="fileSet" format="prims.fileset.zip" /> | |
237 </change_format> | |
238 </data> | |
239 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"> </data> | |
240 <data name="outTsv" format="tabular" label="${tool.name} on ${on_string} - TSV report"> </data> | |
241 </outputs> | |
242 <tests> | |
243 <test> | |
244 </test> | |
245 </tests> | |
246 <help> | |
247 | |
248 .. class:: infomark | |
249 | |
250 This tool searches MS/MS spectra against a database using X!Tandem. | |
251 | |
252 For a complete set of parameters and their default values see `the X!Tandem parameters documentation page`_ . | |
253 Parameters that are not | |
254 made available in the UI above but are listed in the given link are submitted with their | |
255 default values. | |
256 | |
257 For more information on the refine step see: `Why should I use "refinement" to find modifications?`_ . | |
258 | |
259 For more information on the expectation value calculation see: | |
260 `A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes`_ | |
261 , David Fenyƶ and Ronald C. Beavis, Anal. Chem., 2003, 75, 768-774. | |
262 This reference describes how peptides are scored by X!Tandem. | |
263 The expectation values on the individual peptides are calculated using this method. | |
264 <!-- Add this from Ron's email ? : | |
265 They are an estimate of the spectrum-to-peptide match E-value associated with the | |
266 null-hypothesis "all spectrum-to-peptide matches are stochasitic". | |
267 --> | |
268 | |
269 .. _the X!Tandem parameters documentation page: http://www.thegpm.org/tandem/api/index.html | |
270 | |
271 .. _Why should I use "refinement" to find modifications?: http://www.thegpm.org/GPM/refine.html | |
272 | |
273 .. _A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes: http://www.ncbi.nlm.nih.gov/pubmed/12622365 | |
274 | |
275 ----- | |
276 | |
277 **Output** | |
278 | |
279 This tools returns the X!Tandem XML output which can be converted to MzIdentML using the DBSearch converter tool. | |
280 | |
281 It also returns an HTML file with the list of peptides and the option to visualize the peptide to spectrum match | |
282 using an embedded spectrum viewer. | |
283 | |
284 .. image:: $PATH_TO_IMAGES/xtandem_results_viewer.png | |
285 | |
286 Last but not least, it returns the list of identifications in TSV (tab separated values) format for users that are satisfied with this | |
287 and do not need further processing steps like protein inference. | |
288 | |
289 For the GPM web UI of X!Tandem see: | |
290 http://ppp.thegpm.org/tandem/thegpm_ppp.html | |
291 | |
292 </help> | |
293 </tool> |