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comparison msclust.xml @ 36:9018657a9f73

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Added "Membership cutoff (0.0 - 1.0)" option
author pieter.lukasse@wur.nl
date Fri, 19 Sep 2014 11:25:09 +0200
parents 0ff22eec3e4b
children 2398cbcac2cb
comparison
equal deleted inserted replaced
35:0ff22eec3e4b 36:9018657a9f73
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 -rtDistTolUnit $potDensFuncType.rt_dist_tol_unit.type 28 -rtDistTolUnit $potDensFuncType.rt_dist_tol_unit.type
29 -rtDistTol $potDensFuncType.rt_dist_tol_unit.pdf_rt_toler 29 -rtDistTol $potDensFuncType.rt_dist_tol_unit.pdf_rt_toler
30 -rtDistanceConfidence $potDensFuncType.pdf_scan_conf 30 -rtDistanceConfidence $potDensFuncType.pdf_scan_conf
31 -peakWidthMax $potDensFuncType.rt_dist_tol_unit.peak_width_max 31 #if $clusteringType.type == "original"
32 -clustMembershipCutoff $clusteringType.clust_membership_cutoff
33 #end if
32 -centrotypesOut $centrotypesOut 34 -centrotypesOut $centrotypesOut
33 -simOut $simOut 35 -simOut $simOut
34 -micOut $micOut 36 -micOut $micOut
35 -mspOut $mspOut 37 -mspOut $mspOut
36 -classOut $classOut 38 -classOut $classOut
96 <option value="1" selected="true">scan nr</option> 98 <option value="1" selected="true">scan nr</option>
97 <option value="2" >(average) micro minutes</option> 99 <option value="2" >(average) micro minutes</option>
98 </param> 100 </param>
99 <when value="1"> 101 <when value="1">
100 <param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans" /> 102 <param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans" />
101 <param name="peak_width_max" type="float" size="10" value="30" label="MAX Peak Width, in scans" help="This parameter is to avoid calculations of correlation
102 between peaks that are too far apart anyway" />
103 </when> 103 </when>
104 <when value="2"> 104 <when value="2">
105 <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 <param name="pdf_rt_toler" type="float" size="10" value="100000" label="Peak Width, in micro minutes" help="e.g. 100,000=6 seconds" />
106 <param name="peak_width_max" type="float" size="10" value="300000" label="MAX Peak Width, in micro minutes" help="This parameter is to avoid calculations of correlation
107 between peaks that are too far apart anyway" />
108 </when> 106 </when>
109 </conditional> 107 </conditional>
110 <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])" /> 108 <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])" />
111 <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" /> 109 <param name="pdf_pears_treshold" type="float" size="10" value="0.8" label="Correlation threshold (0.0 - 1.0)" />
112 <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])" /> 110 <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])" />
126 <param name="type" type="select" label="Classify using ==========================================================="> 124 <param name="type" type="select" label="Classify using ===========================================================">
127 <option value="original" selected="true">Original - Fuzzy clustering, keep original centers and REUSE (scan distance) tolerances</option> 125 <option value="original" selected="true">Original - Fuzzy clustering, keep original centers and REUSE (scan distance) tolerances</option>
128 <option value="fuzzyCMeans">(experimental) Fuzzy C-Means - Fuzzy clustering, optimize centers</option> 126 <option value="fuzzyCMeans">(experimental) Fuzzy C-Means - Fuzzy clustering, optimize centers</option>
129 </param> 127 </param>
130 <when value="original"> 128 <when value="original">
131 <!-- nothing --> 129 <param name="clust_membership_cutoff" type="float" size="10" value=""
130 label="Membership cutoff (0.0 - 1.0)"
131 help="Items with membership below this value are NOT added to the cluster"/>
132 </when> 132 </when>
133 <!-- one idea would be to have clustering specific tolerance values, not reusing the centrotype selection ones 133 <!-- one idea would be to have clustering specific tolerance values, not reusing the centrotype selection ones
134 <when value="originalNewTol"> 134 <when value="originalNewTol">
135 <param name="clust_scan_toler" type="float" size="10" value="10" label="Peak Width, in scans" /> 135 <param name="clust_scan_toler" type="float" size="10" value="10" label="Peak Width, in scans" />
136 <param name="clust_scan_slope" type="float" size="10" value="2" label="Peak Width margin softness" /> 136 <param name="clust_scan_slope" type="float" size="10" value="2" label="Peak Width margin softness" />