Mercurial > repos > galaxyp > msi_qualitycontrol
changeset 3:f6aa0cff777c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
| author | galaxyp |
|---|---|
| date | Sat, 24 Feb 2018 12:48:28 -0500 |
| parents | 1ccbda92b76b |
| children | fef8bd551236 |
| 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, 15 insertions(+), 7 deletions(-) [+] |
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--- a/msi_qualitycontrol.xml Fri Nov 24 18:08:38 2017 -0500 +++ b/msi_qualitycontrol.xml Sat Feb 24 12:48:28 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.7.0.1"> +<tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.7.0.2"> <description> mass spectrometry imaging QC </description> @@ -159,7 +159,7 @@ "Baseline reduction", "Peak picking", "Centroided", - "# valid input masses") + paste0("# valid masses in ", "$filename")) values = c(paste0(maxfeatures), paste0(minmz, " - ", maxmz), @@ -176,7 +176,7 @@ paste0(baselinereductioninfo), paste0(peakpickinginfo), paste0(centroidedinfo), - paste0(length(inputmasses))) + paste0(length(inputmasses), "/", length(calibrant_list[,1])+length(input_list[,1]))) property_df = data.frame(properties, values) @@ -287,6 +287,12 @@ mass2 = $foldchanges.mass2 distance = $foldchanges.distance + #if not str($foldchanges.filenameratioplot).strip(): + #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2) + #else: + #set $label = $foldchanges.filenameratioplot + #end if + ### find rows which contain masses: mzrowdown1 = features(msidata, mz = mass1-distance) @@ -339,8 +345,8 @@ ratiomatrix = cbind(foldchange, coord(msidata)) print(ggplot(ratiomatrix, aes(x=x, y=y, fill=foldchange), colour=colo) - +scale_y_reverse() + geom_tile() + coord_fixed() - + ggtitle(paste0("Fold change ", mass1, " Da / ", mass2, " Da")) + + geom_tile() + coord_fixed() + + ggtitle("$label") + theme_bw() + theme(text=element_text(family="ArialMT", face="bold", size=12)) + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange") @@ -350,11 +356,12 @@ ## 3) Calibrant images: + par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=0) if (length(inputmasses) != 0) { for (mass in 1:length(inputmasses)) { image(msidata, mz=inputmasses[mass], plusminus=$plusminusinDalton, - main= paste0("3",LETTERS[mass], ") ", inputnames[mass], " (", round(inputmasses[mass], digits = 2), " Da)"), + main= paste0("3", LETTERS[mass], ") ", inputnames[mass], " (", round(inputmasses[mass], digits = 2)," ± ", $plusminusinDalton, " Da)"), contrast.enhance = "histogram", ylim=c(maxy+1, 0)) } } else {print("3) The inputpeptide masses were outside the mass range")} @@ -559,7 +566,7 @@ ]]></configfile> </configfiles> <inputs> - <param name="infile" type="data" format="imzml, rdata, analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" + <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData" help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/> <param name="filename" type="text" value="" optional="true" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name."/> <param name="inputpeptidefile" type="data" optional="true" format="txt, csv" label="Text file with peptidemasses and names" @@ -572,6 +579,7 @@ <param name="mass1" value="1111" type="float" label="Mass 1" help="First mass in Dalton"/> <param name="mass2" value="2222" type="float" label="Mass 2" help="Second mass in Dalton"/> <param name="distance" value="0.25" type="float" label="Distance in Dalton" help="Distance in Da used to find peak maximum from input masses in both directions"/> + <param name="filenameratioplot" type="text" optional="true" label="Title" help="Optional title for fold change plot."/> </repeat> </inputs> <outputs>