Mercurial > repos > pieterlukasse > prims_metabolomics
changeset 60:35f506f30ae4
fixed small rule in pdfread, and other small enhancements
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Fri, 19 Dec 2014 11:30:22 +0100 |
| parents | 458e05d1d172 |
| children | d685210eef3e |
| files | rankfilter_GCMS/pdfread.py xcms_get_alignment_eic.r xcms_get_alignment_eic.xml xcms_get_mass_eic.xml |
| diffstat | 4 files changed, 9 insertions(+), 5 deletions(-) [+] |
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--- a/rankfilter_GCMS/pdfread.py Fri Dec 12 12:28:08 2014 +0100 +++ b/rankfilter_GCMS/pdfread.py Fri Dec 19 11:30:22 2014 +0100 @@ -75,7 +75,7 @@ # replaces of known cases by the same with a white space: name_tmp = name_tmp.replace('lC', 'l C').replace(']C', '] C').replace('sC', 's C').replace('9C', '9 C').replace('.C', '. C') name_tmp = name_tmp.replace(')C', ') C').replace('eC', 'e C').replace('yC', 'y C').replace('oC', 'o C').replace('-C', '- C').replace('dC', 'd C').replace('rC', 'r C') - name_tmp = name_tmp.replace('-, LC', '-, L C').replace('-, DC', '-, D C') + name_tmp = name_tmp.replace(', LC', ', L C').replace(', DC', ', D C') name.append((' '.join(name_tmp.split(' ')[0:len(name_tmp) - 1])).replace(" ", " ")) if name_tmp:
--- a/xcms_get_alignment_eic.r Fri Dec 12 12:28:08 2014 +0100 +++ b/xcms_get_alignment_eic.r Fri Dec 19 11:30:22 2014 +0100 @@ -124,7 +124,7 @@ write(paste("<img src='", "figure", i,".png' />", sep="") , file=args.htmlReportFile, append=TRUE) - png( figureName, type="cairo" ) + png( figureName, type="cairo", width=800 ) plot(eiccor, xsetData, groupidx = i) devname = dev.off()
--- a/xcms_get_alignment_eic.xml Fri Dec 12 12:28:08 2014 +0100 +++ b/xcms_get_alignment_eic.xml Fri Dec 19 11:30:22 2014 +0100 @@ -30,11 +30,12 @@ help="Comma or line-separated list of sample names. Optional field where you can specify the subset of samples to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." > <sanitizer> - <!-- this translates from line-separated to comma separated list --> + <!-- this translates from line-separated to comma separated list, removes quotes --> <valid/> <mapping initial="none"> <add source=" " target=","/> <add source=" " target=""/> + <add source=""" target=""/> </mapping> </sanitizer> </param>
--- a/xcms_get_mass_eic.xml Fri Dec 12 12:28:08 2014 +0100 +++ b/xcms_get_mass_eic.xml Fri Dec 19 11:30:22 2014 +0100 @@ -16,7 +16,7 @@ #else -1 -1 - $massParameters.mzList + "$massParameters.mzList" $massParameters.mzTolPpm #end if "$sampleNames" @@ -43,11 +43,12 @@ <param name="mzList" type="text" area="true" size="7x70" label="m/z list" help="Comma or line-separated list of m/z values for which to plot an EIC. One EIC will be plotted for each m/z given here."> <sanitizer> - <!-- this translates from line-separated to comma separated list --> + <!-- this translates from line-separated to comma separated list, removes quotes --> <valid/> <mapping initial="none"> <add source=" " target=","/> <add source=" " target=""/> + <add source=""" target=""/> </mapping> </sanitizer> </param> @@ -65,10 +66,12 @@ help="Comma or line-separated list of sample names. Here you can specify the subset of samples to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." > <sanitizer> + <!-- this translates from line-separated to comma separated list, removes quotes --> <valid/> <mapping initial="none"> <add source=" " target=","/> <add source=" " target=""/> + <add source=""" target=""/> </mapping> </sanitizer> </param>