Mercurial > repos > galaxyp > msi_qualitycontrol
changeset 5:ac786240ef07 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
| author | galaxyp |
|---|---|
| date | Sun, 11 Mar 2018 10:38:43 -0400 |
| parents | fef8bd551236 |
| children | 5c63fe03ed9e |
| files | msi_qualitycontrol.xml test-data/LM8_file16output.pdf test-data/Testfile_qualitycontrol_analyze75.pdf test-data/Testfile_qualitycontrol_imzml.pdf test-data/Testfile_qualitycontrol_rdata.pdf |
| diffstat | 5 files changed, 16 insertions(+), 27 deletions(-) [+] |
line wrap: on
line diff
--- a/msi_qualitycontrol.xml Thu Mar 01 08:25:48 2018 -0500 +++ b/msi_qualitycontrol.xml Sun Mar 11 10:38:43 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.7.0.3"> +<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.7.0.4"> <description> mass spectrometry imaging QC </description> @@ -120,10 +120,11 @@ ### calculate how many input peptide masses are valid: inputpeptides = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,] number_peptides_in = length(input_list[,1]) - number_peptides_valid = length(inputpeptides) + number_peptides_valid = length(inputpeptides[,1]) #else - inputpeptides = data.frame(0,0) + ###inputpeptides = data.frame(0,0) + inputpeptides = as.data.frame(matrix(, nrow = 0, ncol = 2)) number_peptides_in = 0 number_peptides_valid = 0 #end if @@ -140,9 +141,12 @@ ### calculate how many input calibrant masses are valid: inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,] number_calibrants_in = length(calibrant_list[,1]) - number_calibrants_valid = length(inputcalibrants) + number_calibrants_valid = length(inputcalibrants[,1]) #else - inputcalibrants = data.frame(0,0) + ###inputcalibrants = data.frame(0,0) + + inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2)) + number_calibrants_in = 0 number_calibrants_valid = 0 #end if @@ -156,6 +160,7 @@ inputnames = inputs_all[,2] + properties = c("Number of mz features", "Range of mz values [Da]", "Number of pixels", @@ -171,8 +176,8 @@ "Baseline reduction", "Peak picking", "Centroided", - paste0("# peptides in ", "$peptide_file.display_name"), - paste0("# calibrants in ", "$calibrant_file.display_name")) + paste0("# peptides in \n", "$peptide_file.display_name"), + paste0("# calibrants in \n", "$calibrant_file.display_name")) values = c(paste0(maxfeatures), paste0(minmz, " - ", maxmz), @@ -369,7 +374,8 @@ main= paste0("3", LETTERS[mass], ") ", inputnames[mass], " (", round(inputmasses[mass], digits = 2)," ± ", $plusminus_dalton, " Da)"), contrast.enhance = "histogram", ylim=c(maximumy+2, 0)) } - } else {print("3) The inputpeptide masses were outside the mass range")} + } else {print("3) The inputpeptide masses were not provided or outside the mass range")} + ## 4) Number of peaks per pixel - image @@ -422,7 +428,7 @@ pca = PCA(msidata, ncomp=2) par(mfrow = c(2,1)) plot(pca, col=c("black", "darkgrey"), main="7) PCA for two components") - image(pca, col=c("black", "white"),ylim=c(maximumy+2, 0)) + image(pca, col=c("black", "white"),ylim=c(maximumy+2, 0), strip=FALSE) ############################# III) properties over acquisition (spectra index)########## @@ -455,21 +461,6 @@ abline(v=median(log(TICs[TICs>0])), col="blue") - ## 10) intensity of chosen peptides over acquisition (pixel index) - - if (length(inputcalibrants[,1]) != 0) - { - par(mfrow = c(3, 2), oma=c(0,0,2,0)) - intensityvector = vector() - for (mzvalue in 1:length(inputcalibrants[,1])) - { - mznumber = features(msidata, mz = inputcalibrants[,1][mzvalue]) - intensityvector = spectra(msidata)[][mznumber,] - plot(intensityvector, main=inputnames[mzvalue], xlab="Spectra index \n (= Acquisition time)") - } - title("10) intensity of calibrants over acquisition", outer=TRUE) - }else{print("10) The inputcalibrant masses were outside the mass range")} - ################################## IV) changes over mz ############################ ################################################################################### @@ -560,7 +551,7 @@ x=x+1 } - }else{print("15) The inputcalibrant masses were outside the mass range")} + }else{print("15) The inputcalibrant masses were not provided or outside the mass range")} dev.off() }else{ @@ -625,8 +616,6 @@ <test> <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/> - <param name="peptide_file" value="inputpeptides.csv" ftype="txt"/> - <param name="calibrant_file" ftype="txt" value="inputcalibrantfile1.txt"/> <param name="plusminus_dalton" value="0.1"/> <param name="filename" value="Testfile_rdata"/> <output name="plots" file="Testfile_qualitycontrol_rdata.pdf" compare="sim_size" delta="20000"/>