Mercurial > repos > pieterlukasse > prims_metabolomics

comparison msclust.xml @ 28:b1015b9241cd

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Added option for using retentionMean (micro minutes) for the time dimension
author pieter.lukasse@wur.nl
date Fri, 09 May 2014 17:07:58 +0200
parents 19d8fd10248e
children 0d534bce8e84
comparison
equal deleted inserted replaced
27:ecd3f6c9e606 28:b1015b9241cd
1 <tool name="MsClust" id="msclust2" version="2.0.3"> 1 <tool name="MsClust" id="msclust2" version="2.0.4">
2 <description>Extracts fragmentation spectra from aligned data</description> 2 <description>Extracts fragmentation spectra from aligned data</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 //////////////////////////
23 -clusterSearchStopCriterium $centerSelectionType.cs_stop_criterion 23 -clusterSearchStopCriterium $centerSelectionType.cs_stop_criterion
24 -pearsonDistTreshold $potDensFuncType.pdf_pears_treshold 24 -pearsonDistTreshold $potDensFuncType.pdf_pears_treshold
25 -pearsonTresholdConfidence $potDensFuncType.pdf_pears_conf 25 -pearsonTresholdConfidence $potDensFuncType.pdf_pears_conf
26 -pearsonPDReductionThreshold $centerSelectionType.cs_pears_pd_reductionTreshold 26 -pearsonPDReductionThreshold $centerSelectionType.cs_pears_pd_reductionTreshold
27 -pearsonPDReductionSlope $centerSelectionType.cs_pears_pd_reductionSlope 27 -pearsonPDReductionSlope $centerSelectionType.cs_pears_pd_reductionSlope
28 -scanDistTol $potDensFuncType.pdf_scan_toler 28 -rtDistTolUnit $potDensFuncType.rt_dist_tol_unit.type
29 -scanDistanceConfidence $potDensFuncType.pdf_scan_conf 29 -rtDistTol $potDensFuncType.rt_dist_tol_unit.pdf_rt_toler
30 -rtDistanceConfidence $potDensFuncType.pdf_scan_conf
30 -centrotypesOut $centrotypesOut 31 -centrotypesOut $centrotypesOut
31 -simOut $simOut 32 -simOut $simOut
32 -micOut $micOut 33 -micOut $micOut
33 -mspOut $mspOut 34 -mspOut $mspOut
34 -classOut $classOut 35 -classOut $classOut
89 <param name="type" type="select" size="30" label="Select PD function type ====================================================="> 90 <param name="type" type="select" size="30" label="Select PD function type =====================================================">
90 <option value="original" selected="true">Original</option> 91 <option value="original" selected="true">Original</option>
91 </param> 92 </param>
92 <when value="original"> 93 <when value="original">
93 <param name="pdf_neighborhoodWindowSize" type="integer" size="10" value="200" label="Effective Peaks" /> 94 <param name="pdf_neighborhoodWindowSize" type="integer" size="10" value="200" label="Effective Peaks" />
94 <param name="pdf_scan_toler" type="float" size="10" value="10" label="Peak Width, in scans" /> 95 <conditional name="rt_dist_tol_unit">
96 <param name="type" type="select" size="30" label="Peak time unit">
97 <option value="1" selected="true">scan nr</option>
98 <option value="2" selected="true">(average) micro minutes</option>
99 </param>
100 <when value="1">
101 <param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans" />
102 </when>
103 <when value="2">
104 <param name="pdf_rt_toler" type="float" size="10" value="100000" label="Peak Width, in micro minutes" help="e.g. 100,000=6 seconds" />
105 </when>
106 </conditional>
95 <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" /> 107 <param name="pdf_scan_conf" type="float" size="10" value="80" label="Peak Width confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />
96 <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" /> 108 <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" />
97 <param name="pdf_pears_conf" type="float" size="10" value="98.0" label="Correlation threshold confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" /> 109 <param name="pdf_pears_conf" type="float" size="10" value="98.0" label="Correlation threshold confidence (0.0 to 99.99)" help="example: 0[no confidence]...50[good guess]...99.9[quite certain])" />
98 </when> 110 </when>
99 </conditional> 111 </conditional>