Mercurial > repos > pieterlukasse > prims_metabolomics
changeset 35:0ff22eec3e4b
added peak_width_max for better performance
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Thu, 18 Sep 2014 14:29:57 +0200 |
| parents | e79a7c32b011 |
| children | 9018657a9f73 |
| files | MsClust.jar msclust.xml |
| diffstat | 2 files changed, 6 insertions(+), 1 deletions(-) [+] |
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--- a/msclust.xml Wed Sep 17 11:31:34 2014 +0200 +++ b/msclust.xml Thu Sep 18 14:29:57 2014 +0200 @@ -7,7 +7,7 @@ TODO in command below: add conditionals according to options of using or NOT the tolerances/thresholds from previous steps --> - <command interpreter="java -jar -Xmx58g "> + <command interpreter="java -jar "> MsClust.jar -peaksFileName $inputPeaks -dataType $dataType @@ -28,6 +28,7 @@ -rtDistTolUnit $potDensFuncType.rt_dist_tol_unit.type -rtDistTol $potDensFuncType.rt_dist_tol_unit.pdf_rt_toler -rtDistanceConfidence $potDensFuncType.pdf_scan_conf + -peakWidthMax $potDensFuncType.rt_dist_tol_unit.peak_width_max -centrotypesOut $centrotypesOut -simOut $simOut -micOut $micOut @@ -97,9 +98,13 @@ </param> <when value="1"> <param name="pdf_rt_toler" type="float" size="10" value="10" label="Peak Width, in scans" /> + <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 + between peaks that are too far apart anyway" /> </when> <when value="2"> <param name="pdf_rt_toler" type="float" size="10" value="100000" label="Peak Width, in micro minutes" help="e.g. 100,000=6 seconds" /> + <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 + between peaks that are too far apart anyway" /> </when> </conditional> <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])" />