Mercurial > repos > pieterlukasse > prims_proteomics
comparison quantifere.xml @ 17:40ec8770780d
* Added support for pepxml (and more specifically for
ProteomeDiscoverer 1.4). Tested with ProteomeDiscoverer 1.4 pepxml.
* Improved HTML report of NapQ tool.
* Fixed issue that was preventing SEDMAT matching from running
in parallel/multi-threaded.
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Mon, 14 Apr 2014 17:11:33 +0200 |
| parents | d1edc7971d48 |
| children | d31c6978d9d0 |
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| 16:d56c18ed0f77 | 17:40ec8770780d |
|---|---|
| 1 <tool name="Quantifere" id="quantifere1" version="1.0.2"> | 1 <tool name="Quantifere" id="quantifere1" version="1.0.3"> |
| 2 <description>Protein Inference by Peptide Quantification patterns</description> | 2 <description>Protein Inference by Peptide Quantification patterns</description> |
| 3 <!-- | 3 <!-- |
| 4 For remote debugging start you listener on port 8000 and use the following as command interpreter: | 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 | 5 java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 |
| 6 ////////////////////////// | 6 ////////////////////////// |
| 59 </when> | 59 </when> |
| 60 <when value="No"> | 60 <when value="No"> |
| 61 </when> | 61 </when> |
| 62 </conditional> | 62 </conditional> |
| 63 | 63 |
| 64 <param name="statisticalMeasuresConfig" type="text" area="true" size="6x70" label="Statistical measures configuration" | 64 <param name="statisticalMeasuresConfig" type="text" area="true" size="8x70" label="Statistical measures configuration" |
| 65 help="Here you may specify the statistical measures that are found in the ms/ms results (e.g. p or e-values). | 65 help="Here you may specify the statistical measures that are found in the ms/ms results (e.g. p or e-values). |
| 66 The format is: SM alias => SM name,type,mode[min/max]. Leaving this configuration out while these are present in the | 66 The format is: SM alias => SM name,type,mode[min/max]. Leaving this configuration out while these are present in the |
| 67 dataset will have the effect that they will be wrongly used as a regular scoring scheme, having effect on for example | 67 dataset will have the effect that they will be wrongly used as a regular scoring scheme, having effect on for example |
| 68 the filter criteria below like 'Minimum number of peptide matches with a score above average' ." | 68 the filter criteria below like 'Minimum number of peptide matches with a score above average' ." |
| 69 value="smXTD => MS:1001330,XSLASH!Tandem:expect,min | 69 value="smXTD => MS:1001330,XSLASH!Tandem:expect,min |
| 70 
pvCSVEX => p_value,CSV_EXPORT,min | 70 
pvCSVEX => p_value,CSV_EXPORT,min |
| 71 
smAUTO_LIKELIHOOD => AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max | 71 
smAUTO_LIKELIHOOD => AUTOMOD_LOGLIKELIHOOD,PLGS/Auto-mod,max |
| 72 
smLIKELIHOOD => LOGLIKELIHOOD,PLGS/Databank-search,max | 72 
smLIKELIHOOD => LOGLIKELIHOOD,PLGS/Databank-search,max |
| 73 
smPercoProb => Percolator: probability,Percolator probability,max | |
| 74 
smPercoPEP => Percolator: PEP,Percolator PEP,min | |
| 75 
smPercoQval => Percolator: q-Value,Percolator q-Value,max | |
| 73 "/> | 76 "/> |
| 74 <!-- keep value attribute above aligned like this to avoid white spaces in the value --> | 77 <!-- keep value attribute above aligned like this to avoid white spaces in the value --> |
| 75 <param name="quantificationDataToUse" type="select" | 78 <param name="quantificationDataToUse" type="select" |
| 76 label="Quantification data to use" | 79 label="Quantification data to use" |
| 77 help="Quantification data to use for the pattern clustering and inference steps. NB: check if the chosen data is also | 80 help="Quantification data to use for the pattern clustering and inference steps. NB: check if the chosen data is also |