Mercurial > repos > pieterlukasse > prims_masscomb
annotate masscomb_dbsearch_xtandem.xml @ 9:c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 07 Feb 2014 11:41:58 +0100 |
| parents | 153e9eb5f2ff |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool name="X!Tandem" id="masscomb_xtandem200" version="2.0.0"> |
| 2 <description>MS/MS DB search</description> | |
| 4 | 3 <requirements> |
| 4 <requirement type="set_environment">XTANDEM_12_10_01_PATH</requirement> | |
| 5 <requirement type="package" version="12.10011">xtandem</requirement> | |
| 6 </requirements> | |
| 0 | 7 <!-- |
| 8 For remote debugging start you listener on port 8000 and use the following as command interpreter: | |
| 9 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 | |
| 10 --> | |
| 11 <command interpreter="java -jar"> | |
| 12 MassComb.jar | |
| 13 -action XTANDEMSEARCH | |
| 14 -outputFile $outputFile | |
| 15 -fileGrouping $fileType.type | |
| 16 -inputFile $fileType.inputFile | |
| 17 -parametersFile $parametersFile | |
| 18 -outputTsv $outTsv | |
| 19 -outReport $htmlReportFile | |
| 20 -outReportPicturesPath $htmlReportFile.files_path | |
| 21 </command> | |
| 22 <inputs> | |
| 23 <conditional name="fileType"> | |
| 24 <param name="type" type="select" label="select MS/MS input type"> | |
| 25 <option value="single" selected="true">single-File</option> | |
| 26 <option value="fileSet">fileSet</option> | |
| 27 </param> | |
| 28 <when value="single"> | |
|
9
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
8
diff
changeset
|
29 <param name="inputFile" type="data" format="mzml,mzxml" label="MS/MS input file (mzml or mzxml)"/> |
| 0 | 30 </when> |
| 31 <when value="fileSet"> | |
| 32 <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/> | |
| 33 </when> | |
| 34 </conditional> | |
| 35 | |
| 36 <param name="precursor_mass_tolerance_lower" type="text" size="30" label="precursor monoisotopic mass_tolerance_lower" value="100" help=""/> | |
| 37 <param name="precursor_mass_tolerance_upper" type="text" size="30" label="precursor monoisotopic mass_tolerance_upper" value="100" help=""/> | |
| 38 <param name="precursor_error_units" type="select" label="precursor_error_units" help=""> | |
| 39 <option value="ppm" selected="true">ppm</option> | |
| 40 <option value="Daltons">Daltons</option> | |
| 41 </param> | |
| 42 <param name="fragment_mass_tolerance" type="text" size="30" label="fragment_mass_tolerance" value="0.4" help=""/> | |
| 43 <param name="fragment_error_units" type="select" label="fragment_error_units" help=""> | |
| 44 <option value="ppm">ppm</option> | |
| 45 <option value="Daltons" selected="true">Daltons</option> | |
| 46 </param> | |
| 47 <param name="database" type="data" format="fasta" label="Protein sequences DB (FASTA)"/> | |
| 48 <!-- | |
| 49 <param name="min_precursor_charge" type="text" size="30" label="min_precursor_charge" value="1" help=""/> | |
| 50 <param name="max_precursor_charge" type="text" size="30" label="max_precursor_charge" value="4" help=""/>--> | |
| 51 <param name="fixed_modifications" type="select" display="checkboxes" multiple="true" label="Complete modifications" help=""> | |
| 52 <option value="57.021464@C">Carbamidomethyl (C)</option> | |
| 53 <option value="57.021464@C,10.008269@R,8.014199@K">Cam+SILAC (8@K,10@R)</option> | |
| 54 <option value="57.021464@C,4.025107@K,6.020129@R">Cam+SILAC (4@K,6@R)</option> | |
| 55 <option value="57.021464@C,4.025107@K,6.020129@R,6.020129@L">Cam+SILAC (4@K,6@R,6@L)</option> | |
| 56 <option value="58.005479@C">Carboxymethyl (C)</option> | |
| 57 <option value="45.987721@C">Methylthio (C)</option> | |
| 58 <option value="47.984744@C">Trioxidation (C)</option> | |
| 59 <option value="442.224991@C">ICAT-D (C)</option> | |
| 60 <option value="450.275205@C">ICAT-D:2H(8) (C)</option> | |
| 61 <option value="227.126991@C">ICAT-C (C)</option> | |
| 62 <option value="236.157185@C">ICAT-C:13C(9) (C)</option> | |
| 63 <option value="58.005479@C">Carboxymethyl (C)</option> | |
| 64 <option value="105.057849@C">Pyridylethyl (C)</option> | |
| 65 <option value="71.037114@C">Propionamide (C)</option> | |
| 66 <option value="125.047679@C">Nethylmaleimide (C)</option> | |
| 67 <option value="144.102063@[,144.102063@K">iTRAQ (N-term,K)</option> | |
| 68 <option value="57.021464@C,144.102063@[,144.102063@K">Cam + iTRAQ (C,N-term,K)</option> | |
| 69 <option value="57.021464@C,224.152478@K,224.152478@[">Cam + TMT (C,K,nt)</option> | |
| 70 <option value="57.021464@C,225.155833@K,225.155833@[">Cam + TMT2plex (C,K,nt)</option> | |
| 71 <option value="57.021464@C,229.1629328@K,229.1629328@[">Cam + TMT6plex (C,K,nt)</option> | |
| 72 <option value="57.021464@C,28.0313@[,28.0313@K">Cam + Dimethyl (C,28@N-term,K)</option> | |
| 73 <option value="57.021464@C,32.0564@[,32.0564@K">Cam + Dimethyl (C,32@N-term,K)</option> | |
| 74 <option value="57.021464@C,36.0757@[,36.0757@K">Cam + Dimethyl (C,36@N-term,K)</option> | |
| 75 <option value="45.987721@C,144.102063@[,144.102063@K">Methylthio + iTRAQ (C,N-term,K)</option> | |
| 76 <option value="45.987721@C,224.152478@K,224.152478@[">Methylthio + TMT (C,K,nt)</option> | |
| 77 <option value="45.987721@C,225.155833@K,225.155833@[">Methylthio + TMT2plex (C,K,nt)</option> | |
| 78 <option value="45.987721@C,229.1629328@K,229.1629328@[">Methylthio + TMT6plex (C,K,nt)</option> | |
| 4 | 79 <option value="14.0156@],14.0156@D,14.0156@E">Methy +14Da (D,E,C-term)</option> |
| 0 | 80 </param> |
| 81 <param name="potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications" help=""> | |
| 82 <option value="15.994915@M">Oxidation (M)</option> | |
| 83 <option value="15.994915@W">Oxidation (W)</option> | |
| 84 <option value="0.984016@N">Deamidation (N)</option> | |
| 85 <option value="0.984016@Q">Deamidation (Q)</option> | |
| 86 <option value="79.966331@S">Phospho (S)</option> | |
| 87 <option value="79.966331@T">Phospho (T)</option> | |
| 88 <option value="79.966331@Y">Phospho (Y)</option> | |
| 89 <option value="79.956815@Y">Sulfo (Y)</option> | |
| 90 <option value="42.010565@K">Acetyl (K)</option> | |
| 91 <option value="43.005814@[">Carbamyl (nt)</option> | |
| 92 <option value="43.005814@K">Carbamyl (K)</option> | |
| 93 <option value="72.021129@[">Carboxyethyl (nt)</option> | |
| 94 <option value="72.021129@K">Carboxyethyl (K)</option> | |
| 95 <option value="57.021464@[">Carbamidomethyl (nt)</option> | |
| 96 <option value="57.021464@K">Carbamidomethyl (K)</option> | |
| 97 <option value="57.021464@C">Carbamidomethyl (C)</option> | |
| 98 <option value="58.005479@C">Carboxymethyl (C)</option> | |
| 99 <option value="45.987721@C">Methylthio (C)</option> | |
| 100 <option value="125.047679@C">Nethylmaleimide (C)</option> | |
| 101 <option value="31.989829@C">Dioxidation (C)</option> | |
| 102 <option value="47.984744@C">Trioxidation (C)</option> | |
| 103 <option value="27.994915@K">formyl (K)</option> | |
| 104 <option value="27.994915@[">formyl (nt)</option> | |
| 105 <option value="114.042927@K">GlyGly (K)</option> | |
| 106 <option value="8.0502@C">ICAT-D:2H(8) (C)</option> | |
| 107 <option value="9.0302@C">ICAT-C:13C(9) (C)</option> | |
| 108 <option value="144.102063@[">iTRAQ (N-term)</option> | |
| 109 <option value="144.102063@K">iTRAQ (K)</option> | |
| 110 <option value="6.020129@L">Label:13C(6) (L)</option> | |
| 111 <option value="6.020129@K">Label:13C(6) (K)</option> | |
| 112 <option value="8.014199@K">Label:13C(6)15N(2) (K)</option> | |
| 113 <option value="6.020129@R">Label:13C(6) (R)</option> | |
| 114 <option value="4.025107@K">Label:2H(4) (K)</option> | |
| 115 <option value="125.047679@C">Nethylmaleimide (C)</option> | |
| 116 <option value="31.005814@C">Sulfinamide (C)</option> | |
| 117 <option value="224.152478@K,224.152478@[">TMT (K,nt)</option> | |
| 118 <option value="225.155833@K,225.155833@[">TMT2plex (K,nt)</option> | |
| 119 <option value="229.1629328@K,229.1629328@[">TMT6plex (K,nt)</option> | |
| 120 </param> | |
| 121 <!-- | |
| 122 <param name="missed_cleavages" type="text" size="30" label="missed_cleavages" value="1" help="Nr. of possible cleavage sites missed by the enzyme"/>--> | |
| 123 <param name="minimum_fragment_mz" type="text" size="30" label="minimum_fragment_mz" value="150" help=""/> | |
| 124 <param name="cleavage_site" type="select" label="cleavage_site" help=""> | |
| 125 <option selected="true" value="[RK]|{P}">trypsin, [RK]|{P}</option> | |
| 126 <option value="[R]|[X]">endo-arg-C, [R]|[X]</option> | |
| 127 <option value="[K]|[X]">endo-lys-C, [K]|[X]</option> | |
| 128 <option value="[E]|[X]">endo-glu-C, [E]|[X]</option> | |
| 129 <option value="[X]|[D]">endo-asp-N, [X]|[D]</option> | |
| 130 <option value="[ED]|[X]">V8, [ED]|[X]</option> | |
| 131 <option value="[FYWL]|{P}">chymotrypsin, [FYWL]|{P}</option> | |
| 132 </param> | |
| 133 <param name="maximum_missed_cleavage_sites" type="integer" size="10" value="1" | |
| 134 label="maximum missed cleavage sites" | |
| 135 help="maximum number of missed cleavage sites allowed within a peptide. For a specific, | |
| 136 aggressive enzyme such as trypsin, the number of missed sites will be low: a value of 1 or 2 is appropriate. | |
| 137 For a non-specific enzyme, such as pepsin, then a value of 50 is more appropriate."/> | |
| 138 <param name="max_valid_expect" type="text" size="30" label="maximum valid expectation value" value="0.1" | |
| 139 help="Max E-Value of a hit to be reported. All results with expectation values less than this value | |
| 140 are considered to be statisitically significant and are recorded. "/> | |
| 141 <conditional name="refinementOpt"> | |
| 142 <param name="refinement" type="select" label="Refine search" help="Select this to enable a second round of more | |
| 143 detailed searching, using only the set of proteins found by the contraints above. E.g. | |
| 144 Rather than entering the 'potential modifications' in the options above, try entering them here only. This is | |
| 145 faster and limits this more thorough searching to a set of proteins for which there is already some evidence."> | |
| 146 <option value="yes">Yes</option> | |
| 147 <option value="no" selected="true">No</option> | |
| 148 </param> | |
| 149 <when value="yes"> | |
| 150 <param name="refine_point_mutation" type="select" label="Allow for point mutations (substitutions)" | |
| 151 help="Test the selected sequences for the possibility of a point mutation in each one of the | |
| 152 peptides generated with the initial cleavage chemistry."> | |
| 153 <option value="yes" selected="true">Yes</option> | |
| 154 <option value="no">No</option> | |
| 155 </param> | |
| 156 <param name="refine_potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications to look for in refined search" help=""> | |
| 157 <option value="15.994915@M">Oxidation (M)</option> | |
| 158 <option value="15.994915@W">Oxidation (W)</option> | |
| 159 <option value="0.984016@N">Deamidation (N)</option> | |
| 160 <option value="0.984016@Q">Deamidation (Q)</option> | |
| 161 <option value="79.966331@S">Phospho (S)</option> | |
| 162 <option value="79.966331@T">Phospho (T)</option> | |
| 163 <option value="79.966331@Y">Phospho (Y)</option> | |
| 164 <option value="79.956815@Y">Sulfo (Y)</option> | |
| 165 <option value="42.010565@K">Acetyl (K)</option> | |
| 166 <option value="43.005814@[">Carbamyl (nt)</option> | |
| 167 <option value="43.005814@K">Carbamyl (K)</option> | |
| 168 <option value="72.021129@[">Carboxyethyl (nt)</option> | |
| 169 <option value="72.021129@K">Carboxyethyl (K)</option> | |
| 170 <option value="57.021464@[">Carbamidomethyl (nt)</option> | |
| 171 <option value="57.021464@K">Carbamidomethyl (K)</option> | |
| 172 <option value="57.021464@C">Carbamidomethyl (C)</option> | |
| 173 <option value="58.005479@C">Carboxymethyl (C)</option> | |
| 174 <option value="45.987721@C">Methylthio (C)</option> | |
| 175 <option value="125.047679@C">Nethylmaleimide (C)</option> | |
| 176 <option value="31.989829@C">Dioxidation (C)</option> | |
| 177 <option value="47.984744@C">Trioxidation (C)</option> | |
| 178 <option value="27.994915@K">formyl (K)</option> | |
| 179 <option value="27.994915@[">formyl (nt)</option> | |
| 180 <option value="114.042927@K">GlyGly (K)</option> | |
| 181 <option value="8.0502@C">ICAT-D:2H(8) (C)</option> | |
| 182 <option value="9.0302@C">ICAT-C:13C(9) (C)</option> | |
| 183 <option value="144.102063@[">iTRAQ (N-term)</option> | |
| 184 <option value="144.102063@K">iTRAQ (K)</option> | |
| 185 <option value="6.020129@L">Label:13C(6) (L)</option> | |
| 186 <option value="6.020129@K">Label:13C(6) (K)</option> | |
| 187 <option value="8.014199@K">Label:13C(6)15N(2) (K)</option> | |
| 188 <option value="6.020129@R">Label:13C(6) (R)</option> | |
| 189 <option value="4.025107@K">Label:2H(4) (K)</option> | |
| 190 <option value="125.047679@C">Nethylmaleimide (C)</option> | |
| 191 <option value="31.005814@C">Sulfinamide (C)</option> | |
| 192 <option value="224.152478@K,224.152478@[">TMT (K,nt)</option> | |
| 193 <option value="225.155833@K,225.155833@[">TMT2plex (K,nt)</option> | |
| 194 <option value="229.1629328@K,229.1629328@[">TMT6plex (K,nt)</option> | |
| 195 </param> | |
| 196 <param name="refine_max_valid_expect" type="text" size="30" label="maximum valid expectation value for identifications coming from refine step" value="0.01" | |
| 197 help="Max E-Value of a 'refine based' hit to be reported. Notice that the default value here is stricter than | |
| 198 the same parameter for 'non-refine based' identifications above. "/> | |
| 199 </when> | |
|
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new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
4
diff
changeset
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200 |
|
153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
4
diff
changeset
|
201 <when value="no"> |
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153e9eb5f2ff
new option in file splitter; small fix in xtandem form
pieter.lukasse@wur.nl
parents:
4
diff
changeset
|
202 </when> |
| 0 | 203 </conditional> |
| 204 <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)."> | |
| 205 <option value="yes">Yes</option> | |
| 206 <option value="no" selected="true">No</option> | |
| 207 <option value="only">Only</option> | |
| 208 </param> | |
| 209 | |
| 210 </inputs> | |
| 211 <configfiles> | |
| 212 <configfile name="parametersFile"><?xml version="1.0" encoding="UTF-8"?> | |
| 213 <tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper"> | |
| 214 <Files/> | |
| 215 <Parameters> | |
| 4 | 216 <Attribute attributeName="xtandemLocation" value="\${XTANDEM_12_10_01_PATH}/bin" type="Unknown" description=""/> |
|
9
c317e0f939df
Made converter more robust and added support for mzXML in xtandem interface
pieter.lukasse@wur.nl
parents:
8
diff
changeset
|
217 <Attribute attributeName="xtandemLocation_dev" value="/home/lukas007/galaxy-dist/tool-data/prims/tandem-linux-13-09-01-1/bin/" type="Unknown" description=""/> |
| 0 | 218 <Attribute attributeName="database" value="${database}" type="Unknown" description=""/> |
| 219 <Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/> | |
| 220 <Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/> | |
| 221 <Attribute attributeName="precursor_error_units" toolSpecificName="spectrum, parent monoisotopic mass error units" value="${precursor_error_units}" type="Unknown" description=""/> | |
| 222 <Attribute attributeName="fragment_mass_tolerance" toolSpecificName="spectrum, fragment monoisotopic mass error" value="${fragment_mass_tolerance}" type="Unknown" description=""/> | |
| 223 <Attribute attributeName="fragment_error_units" toolSpecificName="spectrum, fragment monoisotopic mass error units" value="${fragment_error_units}" type="Unknown" description=""/> | |
| 224 <Attribute attributeName="fixed_modifications" toolSpecificName="residue, modification mass" value="${fixed_modifications}" type="Unknown" description=""/> | |
| 225 <Attribute attributeName="potential_modifications" toolSpecificName="residue, potential modification mass" value="${potential_modifications}" type="Unknown" description=""/> | |
| 226 <Attribute attributeName="minimum_fragment_mz" toolSpecificName="spectrum, minimum fragment mz" value="${minimum_fragment_mz}" type="Unknown" description=""/> | |
| 227 <Attribute attributeName="cleavage_site" toolSpecificName="protein, cleavage site" value="${cleavage_site}" type="Unknown" description=""/> | |
| 228 <Attribute attributeName="maximum_missed_cleavage_sites" toolSpecificName="scoring, maximum missed cleavage sites" value="${maximum_missed_cleavage_sites}" type="Unknown" description=""/> | |
| 229 <Attribute attributeName="max_valid_expect" toolSpecificName="output, maximum valid expectation value" value="${max_valid_expect}" type="Unknown" description=""/> | |
| 230 <Attribute attributeName="refinement" toolSpecificName="refine" value="${refinementOpt.refinement}" type="Unknown" description=""/> | |
| 231 #if $refinementOpt.refinement == "yes" | |
| 232 <Attribute attributeName="refine_point_mutation" toolSpecificName="refine, point mutations" value="${refinementOpt.refine_point_mutation}" type="Unknown" description=""/> | |
| 233 <Attribute attributeName="refine_potential_modifications" toolSpecificName="refine, potential modification mass" value="${refinementOpt.refine_potential_modifications}" type="Unknown" description=""/> | |
| 234 <Attribute attributeName="refine_max_valid_expect" toolSpecificName="refine, maximum valid expectation value" value="${refinementOpt.refine_max_valid_expect}" type="Unknown" description=""/> | |
| 235 #end if | |
| 236 <Attribute attributeName="reverse_scoring" toolSpecificName="scoring, include reverse" value="${reverse_scoring}" type="Unknown" description=""/> | |
| 237 </Parameters> | |
| 238 </tns:Program> | |
| 239 </configfile> | |
| 240 </configfiles> | |
| 241 <outputs> | |
| 242 <data name="outputFile" format="bioml" label="${tool.name} on ${on_string} - Results XML"> | |
| 243 <change_format> | |
| 244 <when input="fileType.type" value="fileSet" format="prims.fileset.zip" /> | |
| 245 </change_format> | |
| 246 </data> | |
| 247 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"> </data> | |
| 248 <data name="outTsv" format="tabular" label="${tool.name} on ${on_string} - TSV report"> </data> | |
| 249 </outputs> | |
| 250 <tests> | |
| 251 <test> | |
| 252 </test> | |
| 253 </tests> | |
| 254 <help> | |
| 255 | |
| 256 .. class:: infomark | |
| 257 | |
| 258 This tool searches MS/MS spectra against a database using X!Tandem. | |
| 259 | |
| 260 For a complete set of parameters and their default values see `the X!Tandem parameters documentation page`_ . | |
| 261 Parameters that are not | |
| 262 made available in the UI above but are listed in the given link are submitted with their | |
| 263 default values. | |
| 264 | |
| 265 For more information on the refine step see: `Why should I use "refinement" to find modifications?`_ . | |
| 266 | |
| 267 For more information on the expectation value calculation see: | |
| 268 `A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes`_ | |
| 269 , David Fenyö and Ronald C. Beavis, Anal. Chem., 2003, 75, 768-774. | |
| 270 This reference describes how peptides are scored by X!Tandem. | |
| 271 The expectation values on the individual peptides are calculated using this method. | |
| 272 <!-- Add this from Ron's email ? : | |
| 273 They are an estimate of the spectrum-to-peptide match E-value associated with the | |
| 274 null-hypothesis "all spectrum-to-peptide matches are stochasitic". | |
| 275 --> | |
| 276 | |
| 277 .. _the X!Tandem parameters documentation page: http://www.thegpm.org/tandem/api/index.html | |
| 278 | |
| 279 .. _Why should I use "refinement" to find modifications?: http://www.thegpm.org/GPM/refine.html | |
| 280 | |
| 281 .. _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 | |
| 282 | |
| 283 ----- | |
| 284 | |
| 285 **Output** | |
| 286 | |
| 287 This tools returns the X!Tandem XML output which can be converted to MzIdentML using the DBSearch converter tool. | |
| 288 | |
| 289 It also returns an HTML file with the list of peptides and the option to visualize the peptide to spectrum match | |
| 290 using an embedded spectrum viewer. | |
| 291 | |
| 292 .. image:: $PATH_TO_IMAGES/xtandem_results_viewer.png | |
| 293 | |
| 294 Last but not least, it returns the list of identifications in TSV (tab separated values) format for users that are satisfied with this | |
| 295 and do not need further processing steps like protein inference. | |
| 296 | |
| 297 For the GPM web UI of X!Tandem see: | |
| 298 http://ppp.thegpm.org/tandem/thegpm_ppp.html | |
| 299 | |
| 300 </help> | |
| 301 </tool> |