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diff masscomb_dbsearch_xtandem.xml @ 0:d6001e8d7441
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| author | pieter.lukasse@wur.nl |
|---|---|
| date | Wed, 08 Jan 2014 11:34:51 +0100 |
| parents | |
| children | b34fb7461546 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/masscomb_dbsearch_xtandem.xml Wed Jan 08 11:34:51 2014 +0100 @@ -0,0 +1,293 @@ +<tool name="X!Tandem" id="masscomb_xtandem200" version="2.0.0"> + <description>MS/MS DB search</description> + <!-- + For remote debugging start you listener on port 8000 and use the following as command interpreter: + java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 + --> + <command interpreter="java -jar"> + MassComb.jar + -action XTANDEMSEARCH + -outputFile $outputFile + -fileGrouping $fileType.type + -inputFile $fileType.inputFile + -parametersFile $parametersFile + -outputTsv $outTsv + -outReport $htmlReportFile + -outReportPicturesPath $htmlReportFile.files_path + </command> +<inputs> + <conditional name="fileType"> + <param name="type" type="select" label="select MS/MS input type"> + <option value="single" selected="true">single-File</option> + <option value="fileSet">fileSet</option> + </param> + <when value="single"> + <param name="inputFile" type="data" format="mzml" label="MS/MS input file (mzml)"/> + </when> + <when value="fileSet"> + <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/> + </when> + </conditional> + + <param name="precursor_mass_tolerance_lower" type="text" size="30" label="precursor monoisotopic mass_tolerance_lower" value="100" help=""/> + <param name="precursor_mass_tolerance_upper" type="text" size="30" label="precursor monoisotopic mass_tolerance_upper" value="100" help=""/> + <param name="precursor_error_units" type="select" label="precursor_error_units" help=""> + <option value="ppm" selected="true">ppm</option> + <option value="Daltons">Daltons</option> + </param> + <param name="fragment_mass_tolerance" type="text" size="30" label="fragment_mass_tolerance" value="0.4" help=""/> + <param name="fragment_error_units" type="select" label="fragment_error_units" help=""> + <option value="ppm">ppm</option> + <option value="Daltons" selected="true">Daltons</option> + </param> + <param name="database" type="data" format="fasta" label="Protein sequences DB (FASTA)"/> + <!-- + <param name="min_precursor_charge" type="text" size="30" label="min_precursor_charge" value="1" help=""/> + <param name="max_precursor_charge" type="text" size="30" label="max_precursor_charge" value="4" help=""/>--> + <param name="fixed_modifications" type="select" display="checkboxes" multiple="true" label="Complete modifications" help=""> + <option value="57.021464@C">Carbamidomethyl (C)</option> + <option value="57.021464@C,10.008269@R,8.014199@K">Cam+SILAC (8@K,10@R)</option> + <option value="57.021464@C,4.025107@K,6.020129@R">Cam+SILAC (4@K,6@R)</option> + <option value="57.021464@C,4.025107@K,6.020129@R,6.020129@L">Cam+SILAC (4@K,6@R,6@L)</option> + <option value="58.005479@C">Carboxymethyl (C)</option> + <option value="45.987721@C">Methylthio (C)</option> + <option value="47.984744@C">Trioxidation (C)</option> + <option value="442.224991@C">ICAT-D (C)</option> + <option value="450.275205@C">ICAT-D:2H(8) (C)</option> + <option value="227.126991@C">ICAT-C (C)</option> + <option value="236.157185@C">ICAT-C:13C(9) (C)</option> + <option value="58.005479@C">Carboxymethyl (C)</option> + <option value="105.057849@C">Pyridylethyl (C)</option> + <option value="71.037114@C">Propionamide (C)</option> + <option value="125.047679@C">Nethylmaleimide (C)</option> + <option value="144.102063@[,144.102063@K">iTRAQ (N-term,K)</option> + <option value="57.021464@C,144.102063@[,144.102063@K">Cam + iTRAQ (C,N-term,K)</option> + <option value="57.021464@C,224.152478@K,224.152478@[">Cam + TMT (C,K,nt)</option> + <option value="57.021464@C,225.155833@K,225.155833@[">Cam + TMT2plex (C,K,nt)</option> + <option value="57.021464@C,229.1629328@K,229.1629328@[">Cam + TMT6plex (C,K,nt)</option> + <option value="57.021464@C,28.0313@[,28.0313@K">Cam + Dimethyl (C,28@N-term,K)</option> + <option value="57.021464@C,32.0564@[,32.0564@K">Cam + Dimethyl (C,32@N-term,K)</option> + <option value="57.021464@C,36.0757@[,36.0757@K">Cam + Dimethyl (C,36@N-term,K)</option> + <option value="45.987721@C,144.102063@[,144.102063@K">Methylthio + iTRAQ (C,N-term,K)</option> + <option value="45.987721@C,224.152478@K,224.152478@[">Methylthio + TMT (C,K,nt)</option> + <option value="45.987721@C,225.155833@K,225.155833@[">Methylthio + TMT2plex (C,K,nt)</option> + <option value="45.987721@C,229.1629328@K,229.1629328@[">Methylthio + TMT6plex (C,K,nt)</option> + <option value="14.0156@],14.0156@D,14.0156@E">Methy +14Da (D,E,C-term)</option> + </param> + <param name="potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications" help=""> + <option value="15.994915@M">Oxidation (M)</option> + <option value="15.994915@W">Oxidation (W)</option> + <option value="0.984016@N">Deamidation (N)</option> + <option value="0.984016@Q">Deamidation (Q)</option> + <option value="79.966331@S">Phospho (S)</option> + <option value="79.966331@T">Phospho (T)</option> + <option value="79.966331@Y">Phospho (Y)</option> + <option value="79.956815@Y">Sulfo (Y)</option> + <option value="42.010565@K">Acetyl (K)</option> + <option value="43.005814@[">Carbamyl (nt)</option> + <option value="43.005814@K">Carbamyl (K)</option> + <option value="72.021129@[">Carboxyethyl (nt)</option> + <option value="72.021129@K">Carboxyethyl (K)</option> + <option value="57.021464@[">Carbamidomethyl (nt)</option> + <option value="57.021464@K">Carbamidomethyl (K)</option> + <option value="57.021464@C">Carbamidomethyl (C)</option> + <option value="58.005479@C">Carboxymethyl (C)</option> + <option value="45.987721@C">Methylthio (C)</option> + <option value="125.047679@C">Nethylmaleimide (C)</option> + <option value="31.989829@C">Dioxidation (C)</option> + <option value="47.984744@C">Trioxidation (C)</option> + <option value="27.994915@K">formyl (K)</option> + <option value="27.994915@[">formyl (nt)</option> + <option value="114.042927@K">GlyGly (K)</option> + <option value="8.0502@C">ICAT-D:2H(8) (C)</option> + <option value="9.0302@C">ICAT-C:13C(9) (C)</option> + <option value="144.102063@[">iTRAQ (N-term)</option> + <option value="144.102063@K">iTRAQ (K)</option> + <option value="6.020129@L">Label:13C(6) (L)</option> + <option value="6.020129@K">Label:13C(6) (K)</option> + <option value="8.014199@K">Label:13C(6)15N(2) (K)</option> + <option value="6.020129@R">Label:13C(6) (R)</option> + <option value="4.025107@K">Label:2H(4) (K)</option> + <option value="125.047679@C">Nethylmaleimide (C)</option> + <option value="31.005814@C">Sulfinamide (C)</option> + <option value="224.152478@K,224.152478@[">TMT (K,nt)</option> + <option value="225.155833@K,225.155833@[">TMT2plex (K,nt)</option> + <option value="229.1629328@K,229.1629328@[">TMT6plex (K,nt)</option> + </param> + <!-- + <param name="missed_cleavages" type="text" size="30" label="missed_cleavages" value="1" help="Nr. of possible cleavage sites missed by the enzyme"/>--> + <param name="minimum_fragment_mz" type="text" size="30" label="minimum_fragment_mz" value="150" help=""/> + <param name="cleavage_site" type="select" label="cleavage_site" help=""> + <option selected="true" value="[RK]|{P}">trypsin, [RK]|{P}</option> + <option value="[R]|[X]">endo-arg-C, [R]|[X]</option> + <option value="[K]|[X]">endo-lys-C, [K]|[X]</option> + <option value="[E]|[X]">endo-glu-C, [E]|[X]</option> + <option value="[X]|[D]">endo-asp-N, [X]|[D]</option> + <option value="[ED]|[X]">V8, [ED]|[X]</option> + <option value="[FYWL]|{P}">chymotrypsin, [FYWL]|{P}</option> + </param> + <param name="maximum_missed_cleavage_sites" type="integer" size="10" value="1" + label="maximum missed cleavage sites" + help="maximum number of missed cleavage sites allowed within a peptide. For a specific, + aggressive enzyme such as trypsin, the number of missed sites will be low: a value of 1 or 2 is appropriate. + For a non-specific enzyme, such as pepsin, then a value of 50 is more appropriate."/> + <param name="max_valid_expect" type="text" size="30" label="maximum valid expectation value" value="0.1" + help="Max E-Value of a hit to be reported. All results with expectation values less than this value + are considered to be statisitically significant and are recorded. "/> + <conditional name="refinementOpt"> + <param name="refinement" type="select" label="Refine search" help="Select this to enable a second round of more + detailed searching, using only the set of proteins found by the contraints above. E.g. + Rather than entering the 'potential modifications' in the options above, try entering them here only. This is + faster and limits this more thorough searching to a set of proteins for which there is already some evidence."> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + </param> + <when value="yes"> + <param name="refine_point_mutation" type="select" label="Allow for point mutations (substitutions)" + help="Test the selected sequences for the possibility of a point mutation in each one of the + peptides generated with the initial cleavage chemistry."> + <option value="yes" selected="true">Yes</option> + <option value="no">No</option> + </param> + <param name="refine_potential_modifications" type="select" display="checkboxes" multiple="true" label="Potential modifications to look for in refined search" help=""> + <option value="15.994915@M">Oxidation (M)</option> + <option value="15.994915@W">Oxidation (W)</option> + <option value="0.984016@N">Deamidation (N)</option> + <option value="0.984016@Q">Deamidation (Q)</option> + <option value="79.966331@S">Phospho (S)</option> + <option value="79.966331@T">Phospho (T)</option> + <option value="79.966331@Y">Phospho (Y)</option> + <option value="79.956815@Y">Sulfo (Y)</option> + <option value="42.010565@K">Acetyl (K)</option> + <option value="43.005814@[">Carbamyl (nt)</option> + <option value="43.005814@K">Carbamyl (K)</option> + <option value="72.021129@[">Carboxyethyl (nt)</option> + <option value="72.021129@K">Carboxyethyl (K)</option> + <option value="57.021464@[">Carbamidomethyl (nt)</option> + <option value="57.021464@K">Carbamidomethyl (K)</option> + <option value="57.021464@C">Carbamidomethyl (C)</option> + <option value="58.005479@C">Carboxymethyl (C)</option> + <option value="45.987721@C">Methylthio (C)</option> + <option value="125.047679@C">Nethylmaleimide (C)</option> + <option value="31.989829@C">Dioxidation (C)</option> + <option value="47.984744@C">Trioxidation (C)</option> + <option value="27.994915@K">formyl (K)</option> + <option value="27.994915@[">formyl (nt)</option> + <option value="114.042927@K">GlyGly (K)</option> + <option value="8.0502@C">ICAT-D:2H(8) (C)</option> + <option value="9.0302@C">ICAT-C:13C(9) (C)</option> + <option value="144.102063@[">iTRAQ (N-term)</option> + <option value="144.102063@K">iTRAQ (K)</option> + <option value="6.020129@L">Label:13C(6) (L)</option> + <option value="6.020129@K">Label:13C(6) (K)</option> + <option value="8.014199@K">Label:13C(6)15N(2) (K)</option> + <option value="6.020129@R">Label:13C(6) (R)</option> + <option value="4.025107@K">Label:2H(4) (K)</option> + <option value="125.047679@C">Nethylmaleimide (C)</option> + <option value="31.005814@C">Sulfinamide (C)</option> + <option value="224.152478@K,224.152478@[">TMT (K,nt)</option> + <option value="225.155833@K,225.155833@[">TMT2plex (K,nt)</option> + <option value="229.1629328@K,229.1629328@[">TMT6plex (K,nt)</option> + </param> + <param name="refine_max_valid_expect" type="text" size="30" label="maximum valid expectation value for identifications coming from refine step" value="0.01" + help="Max E-Value of a 'refine based' hit to be reported. Notice that the default value here is stricter than + the same parameter for 'non-refine based' identifications above. "/> + </when> + </conditional> + <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)."> + <option value="yes">Yes</option> + <option value="no" selected="true">No</option> + <option value="only">Only</option> + </param> + +</inputs> +<configfiles> +<configfile name="parametersFile"><?xml version="1.0" encoding="UTF-8"?> +<tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="XTandemWrapper" program="XTandemWrapper"> + <Files/> + <Parameters> + <Attribute attributeName="xtandemLocation" value="/home/lukas007/galaxy-dist/tool-data/prims/tandem-linux-12-10-01-1/bin/" type="Unknown" description=""/> + <Attribute attributeName="database" value="${database}" type="Unknown" description=""/> + <Attribute attributeName="precursor_mass_tolerance_lower" toolSpecificName="spectrum, parent monoisotopic mass error minus" value="${precursor_mass_tolerance_lower}" type="Unknown" description=""/> + <Attribute attributeName="precursor_mass_tolerance_upper" toolSpecificName="spectrum, parent monoisotopic mass error plus" value="${precursor_mass_tolerance_upper}" type="Unknown" description=""/> + <Attribute attributeName="precursor_error_units" toolSpecificName="spectrum, parent monoisotopic mass error units" value="${precursor_error_units}" type="Unknown" description=""/> + <Attribute attributeName="fragment_mass_tolerance" toolSpecificName="spectrum, fragment monoisotopic mass error" value="${fragment_mass_tolerance}" type="Unknown" description=""/> + <Attribute attributeName="fragment_error_units" toolSpecificName="spectrum, fragment monoisotopic mass error units" value="${fragment_error_units}" type="Unknown" description=""/> + <Attribute attributeName="fixed_modifications" toolSpecificName="residue, modification mass" value="${fixed_modifications}" type="Unknown" description=""/> + <Attribute attributeName="potential_modifications" toolSpecificName="residue, potential modification mass" value="${potential_modifications}" type="Unknown" description=""/> + <Attribute attributeName="minimum_fragment_mz" toolSpecificName="spectrum, minimum fragment mz" value="${minimum_fragment_mz}" type="Unknown" description=""/> + <Attribute attributeName="cleavage_site" toolSpecificName="protein, cleavage site" value="${cleavage_site}" type="Unknown" description=""/> + <Attribute attributeName="maximum_missed_cleavage_sites" toolSpecificName="scoring, maximum missed cleavage sites" value="${maximum_missed_cleavage_sites}" type="Unknown" description=""/> + <Attribute attributeName="max_valid_expect" toolSpecificName="output, maximum valid expectation value" value="${max_valid_expect}" type="Unknown" description=""/> + <Attribute attributeName="refinement" toolSpecificName="refine" value="${refinementOpt.refinement}" type="Unknown" description=""/> + #if $refinementOpt.refinement == "yes" + <Attribute attributeName="refine_point_mutation" toolSpecificName="refine, point mutations" value="${refinementOpt.refine_point_mutation}" type="Unknown" description=""/> + <Attribute attributeName="refine_potential_modifications" toolSpecificName="refine, potential modification mass" value="${refinementOpt.refine_potential_modifications}" type="Unknown" description=""/> + <Attribute attributeName="refine_max_valid_expect" toolSpecificName="refine, maximum valid expectation value" value="${refinementOpt.refine_max_valid_expect}" type="Unknown" description=""/> + #end if + <Attribute attributeName="reverse_scoring" toolSpecificName="scoring, include reverse" value="${reverse_scoring}" type="Unknown" description=""/> + </Parameters> +</tns:Program> +</configfile> +</configfiles> +<outputs> + <data name="outputFile" format="bioml" label="${tool.name} on ${on_string} - Results XML"> + <change_format> + <when input="fileType.type" value="fileSet" format="prims.fileset.zip" /> + </change_format> + </data> + <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - HTML report"> </data> + <data name="outTsv" format="tabular" label="${tool.name} on ${on_string} - TSV report"> </data> +</outputs> +<tests> + <test> + </test> +</tests> +<help> + +.. class:: infomark + +This tool searches MS/MS spectra against a database using X!Tandem. + +For a complete set of parameters and their default values see `the X!Tandem parameters documentation page`_ . +Parameters that are not +made available in the UI above but are listed in the given link are submitted with their +default values. + +For more information on the refine step see: `Why should I use "refinement" to find modifications?`_ . + +For more information on the expectation value calculation see: +`A Method for Assessing the Statistical Significance of Mass Spectrometry-Based Protein Identifications Using General Scoring Schemes`_ +, David Fenyö and Ronald C. Beavis, Anal. Chem., 2003, 75, 768-774. +This reference describes how peptides are scored by X!Tandem. +The expectation values on the individual peptides are calculated using this method. +<!-- Add this from Ron's email ? : +They are an estimate of the spectrum-to-peptide match E-value associated with the +null-hypothesis "all spectrum-to-peptide matches are stochasitic". +--> + +.. _the X!Tandem parameters documentation page: http://www.thegpm.org/tandem/api/index.html + +.. _Why should I use "refinement" to find modifications?: http://www.thegpm.org/GPM/refine.html + +.. _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 + +----- + +**Output** + +This tools returns the X!Tandem XML output which can be converted to MzIdentML using the DBSearch converter tool. + +It also returns an HTML file with the list of peptides and the option to visualize the peptide to spectrum match +using an embedded spectrum viewer. + +.. image:: $PATH_TO_IMAGES/xtandem_results_viewer.png + +Last but not least, it returns the list of identifications in TSV (tab separated values) format for users that are satisfied with this +and do not need further processing steps like protein inference. + +For the GPM web UI of X!Tandem see: +http://ppp.thegpm.org/tandem/thegpm_ppp.html + +</help> +</tool> \ No newline at end of file