msi_spectra_plot: msi_spectra_plots.xml comparison

comparison msi_spectra_plots.xml @ 2:ea4f1c516368 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_spectra_plots commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0

author	galaxyp
date	Mon, 28 May 2018 12:39:59 -0400
parents	7caaf84a8a51
children	fe28ca73548a

comparison

equal deleted inserted replaced

-:7caaf84a8a51
+:ea4f1c516368
-<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.7.0.1">
+<tool id="mass_spectrometry_imaging_mzplots" name="MSI plot spectra" version="1.10.0.0">
 <description>
 mass spectrometry imaging mass spectra plots
 </description>
 <requirements>
-<requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>
+<requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
 <requirement type="package" version="2.2.1">r-gridextra</requirement>
-<requirement type="package" version="2.23-15">r-kernsmooth</requirement>
 </requirements>
 <command detect_errors="exit_code">
 <![CDATA[
 #if $infile.ext == 'imzml'
-cp '${infile.extra_files_path}/imzml' infile.imzML &&
+ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
-cp '${infile.extra_files_path}/ibd' infile.ibd &&
+ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
 #elif $infile.ext == 'analyze75'
-cp '${infile.extra_files_path}/hdr' infile.hdr &&
+ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
-cp '${infile.extra_files_path}/img' infile.img &&
+ln -s '${infile.extra_files_path}/img' infile.img &&
-cp '${infile.extra_files_path}/t2m' infile.t2m &&
+ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
 #else
 ln -s $infile infile.RData &&
 #end if
 cat '${MSI_mzplots}' &&
 Rscript '${MSI_mzplots}'
 ]]>
 </command>
 <configfiles>
 <configfile name="MSI_mzplots"><![CDATA[
-################################# load libraries and read file #########################
+################################# load libraries and read file #################
 library(Cardinal)
 library(gridExtra)
-library(KernSmooth)
 ## Read MALDI Imaging dataset
 #if $infile.ext == 'imzml'
-msidata <- readMSIData('infile.imzML')
+msidata = readImzML('infile')
 #elif $infile.ext == 'analyze75'
-msidata <- readMSIData('infile.hdr')
+msidata = readAnalyze('infile')
 #else
 load('infile.RData')
 #end if
-###################################### file properties in numbers ######################
+###################################### file properties in numbers ##############
 ## Number of features (mz)
 maxfeatures = length(features(msidata))
 ## Range mz
 minmz = round(min(mz(msidata)), digits=2)
 paste0(peakpickinginfo),
 paste0(centroidedinfo))
 property_df = data.frame(properties, values)
+print("before pdf")
-######################################## PDF #############################################
-##########################################################################################
+######################################## PDF ###################################
-##########################################################################################
+################################################################################
+################################################################################
 pdf("mzplots.pdf", fonts = "Times", pointsize = 12)
 plot(0,type='n',axes=FALSE,ann=FALSE)
 title(main=paste0("Plotted mass spectra for file: \n\n", "$infile.display_name"))
-############################# I) numbers ####################################
+############################# I) numbers ######################################
-#############################################################################
+###############################################################################
+print("in pdf")
 grid.table(property_df, rows= NULL)
-counting = 2
-outputmatrix = matrix(mz(msidata), ncol=1, byrow=TRUE)
-colnames(outputmatrix) = "m/z"
 if (npeaks > 0)
 {
 pixeldf = data.frame(matrix(ncol = 2, nrow=0))
-#for $chosenpixel in $repeatpixel:
+#if str( $pixel_conditional.pixel_type) == 'single_pixel':
+print("single_pixel")
-### is x and y which was put in to define pixel valid coordinates?
-pixelisvalid = as.character($chosenpixel.inputx %in% coord(msidata)\$x & $chosenpixel.inputy %in% coord(msidata)\$y)
+#for $chosenpixel in $pixel_conditional.repeatpixel:
-pixelname = paste0("x=", $chosenpixel.inputx,", ", "y=", $chosenpixel.inputy)
-pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
+pixelisvalid = as.character($chosenpixel.inputx %in% coord(msidata)\$x & $chosenpixel.inputy %in% coord(msidata)\$y)
+pixelname = paste0("x=", $chosenpixel.inputx,", ", "y=", $chosenpixel.inputy)
-############################# II) control image #############################
+print(pixelname)
-#############################################################################
+print(colnames(pixeldf))
+print(colnames(cbind(pixelname, pixelisvalid)))
+pixeldf = rbind(pixeldf, cbind(pixelname, pixelisvalid))
-if (pixelisvalid == "TRUE")
+print(colnames(pixeldf))
-{
+############################# II) control image ####################
+####################################################################
-image(msidata, mz=$chosenpixel.inputmz,
-ylim = c(maximumy+(0.2*maximumy),minimumy-1),colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, contrast.enhance = "histogram",
-main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy))
+if (pixelisvalid == "TRUE")
+{
-abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
-abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
+print(pixelisvalid)
-##################### III) plot full mass spectrum ##########################
+image(msidata, mz=$chosenpixel.inputmz,
-#############################################################################
+ylim = c(maximumy+(0.2*maximumy),minimumy-1),colorkey=FALSE, plusminus = $chosenpixel.plusminusinDalton, contrast.enhance = "histogram",
+main= paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy))
-plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))
+abline(v=$chosenpixel.inputx, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
+abline(h=$chosenpixel.inputy, col ="$chosenpixel.inputcolour", lty="$chosenpixel.inputtype", lwd=$chosenpixel.inputwidth)
-##################### IV) plot zoom-in mass spectrum ##########################
-#############################################################################
+##################### III) plot full mass spectrum #################
+####################################################################
-#if $chosenpixel.zoomedplot:
-#for $token in $chosenpixel.zoomedplot:
+plot(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))
+##################### IV) plot zoom-in mass spectrum ###############
+####################################################################
+#if $chosenpixel.zoomedplot:
+#for $token in $chosenpixel.zoomedplot:
+minmasspixel = features(msidata, mz=$token.xlimmin)
+maxmasspixel = features(msidata, mz=$token.xlimmax)
+plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy),
+xlim= c($token.xlimmin,$token.xlimmax))
+#end for
+#end if
+}else{
+print("The pixel coordinates did not correspond to a real pixel")}
+#end for
+colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
+#elif str( $pixel_conditional.pixel_type) == 'sample_pixel':
+print("sample_pixel")
+##################### I) Sample: plot full mass spectrum ###########
+plot(msidata, pixel=1:ncol(msidata), pixel.groups=pData(msidata)\$sample, key=TRUE, col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE)
+##################### II) Sample: plot zoom-in mass spectrum #######
+#if $pixel_conditional.zoomed_sample:
+#for $token in $pixel_conditional.zoomed_sample:
 minmasspixel = features(msidata, mz=$token.xlimmin)
 maxmasspixel = features(msidata, mz=$token.xlimmax)
+plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),  xlim= c($token.xlimmin,$token.xlimmax),pixel.groups=pData(msidata)\$sample, key=TRUE,col=c("blue", "orange", "green", "red", "yellow", "grey"), superpose=TRUE)
-plot(msidata[minmasspixel:maxmasspixel,], coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy),
-xlim= c($token.xlimmin,$token.xlimmax))
 #end for
 #end if
-##################### V) Output with mz and intensities #####################
+pixeldf = data.frame(table(pData(msidata)\$sample))
-#############################################################################
+colnames(pixeldf) = c("sample name", "number of pixels")
+#end if
-### for each repeat a new intensity column for the new pixel is added
-outputmatrix = cbind(outputmatrix, spectra(msidata)[,pixels(msidata, coord=list(x=$chosenpixel.inputx, y=$chosenpixel.inputy))])
-colnames(outputmatrix)[counting] = paste0("x= ",$chosenpixel.inputx, ", y= ", $chosenpixel.inputy, " intensity")
-counting = counting+1
-}else{
-print("These pixel coordinates did not correspond to a real pixel")}
-#end for
-colnames(pixeldf) = c("pixel coordinates", "coordinates were found in this file")
 plot(0,type='n',axes=FALSE,ann=FALSE)
-title(main=paste0("Overview of chosen pixel for file:\n", "$infile.display_name"))
+title(main="Overview of chosen pixel:")
 grid.table(pixeldf, rows= NULL)
 dev.off()
-write.table(outputmatrix, file="$tabularmatrix", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
 }else{
 print("Inputfile has no intensities > 0")
 dev.off()
 }
 ]]></configfile>
 </configfiles>
 <inputs>
 <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)"/>
-<repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20">
+<conditional name="pixel_conditional">
-<param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/>
+<param name="pixel_type" type="select" label="Select if you want to plot the mass spectrum of a single pixel or of all pixels of a sample">
-<param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/>
+<option value="single_pixel" selected="True">Single pixel</option>
-<param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, here mz in Dalton" help="mz will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/>
+<option value="sample_pixel">All pixels of a sample</option>
-<param name="plusminusinDalton" value="0.25" type="float" label="mass range for this mz value" help="plusminus mass window in Dalton"/>
-<param name="inputcolour" type="select" label="select the colour for the lines at x and y position">
-<option value="white" selected="True">white</option>
-<option value="black">black</option>
-<option value="grey">grey</option>
-<option value="blue">blue</option>
-<option value="red">red</option>
-<option value="green">green</option>
 </param>
-<param name="inputtype" type="select" label="select the line type for the lines at x and y position">
+<when value="single_pixel">
-<option value="solid" selected="True">solid</option>
+<repeat name="repeatpixel" title="Plot mass spectra for pixel of interest" min="1" max="20">
-<option value="dashed">dashed</option>
+<param name="inputx" type="integer" value="" label="x-coordinate of pixel of interest" help="x-value of the pixel of interest"/>
-<option value="dotted">dotted</option>
+<param name="inputy" type="integer" value="" label="y-coordinate of pixel of interest" help="y-value of the pixel of interest"/>
-<option value="longdash">longdash</option>
+<param name="inputmz" type="float" value="1296.7" label="Next parameters are to control heatmap image which will be plotted, here mz in Dalton" help="mz will be displayed as heatmap and the pixel of interest will be visualized by the intersection of two lines"/>
-</param>
+<param name="plusminusinDalton" value="0.25" type="float" label="mass range for this mz value" help="plusminus mass window in Dalton"/>
-<param name="inputwidth" type="integer" value="2" label="select the width of the lines at x and y position"/>
+<param name="inputcolour" type="select" label="select the colour for the lines at x and y position">
-<repeat name="zoomedplot" title="Zoomed in plots with mz min and mz max to define the plot window" min="0" max="50">
+<option value="white" selected="True">white</option>
-<param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum mz for zoomed in window"/>
+<option value="black">black</option>
-<param name="xlimmax" type="integer" value="" label="upper boundary in Dalton for plotting window" help="maximum mz for zoomed in window"/>
+<option value="grey">grey</option>
-</repeat>
+<option value="blue">blue</option>
-</repeat>
+<option value="red">red</option>
+<option value="green">green</option>
+</param>
+<param name="inputtype" type="select" label="select the line type for the lines at x and y position">
+<option value="solid" selected="True">solid</option>
+<option value="dashed">dashed</option>
+<option value="dotted">dotted</option>
+<option value="longdash">longdash</option>
+</param>
+<param name="inputwidth" type="integer" value="2" label="select the width of the lines at x and y position"/>
+<repeat name="zoomedplot" title="Zoomed in plots with mz min and mz max to define the plot window" min="0" max="50">
+<param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum mz for zoomed in window"/>
+<param name="xlimmax" type="integer" value="" label="upper boundary in Dalton for plotting window" help="maximum mz for zoomed in window"/>
+</repeat>
+</repeat>
+</when>
+<when value="sample_pixel">
+<repeat name="zoomed_sample" title="Zoomed in plots with mz min and mz max to define the plot window" min="0" max="50">
+<param name="xlimmin" type="integer" value="" label="lower boundary in Dalton for plotting window" help="minimum mz for zoomed in window"/>
+<param name="xlimmax" type="integer" value="" label="upper boundary in Dalton for plotting window" help="maximum mz for zoomed in window"/>
+</repeat>
+</when>
+</conditional>
 </inputs>
 <outputs>
 <data format="pdf" name="plots" from_work_dir="mzplots.pdf" label = "${tool.name} ${on_string}"/>
-<data format="tabular" name="tabularmatrix" label="Mass spectrum ${on_string}" />
 </outputs>
 <tests>
 <test>
 <param name="infile" value="" ftype="imzml">
 <composite_data value="Example_Continuous.imzML"/>
 <composite_data value="Example_Continuous.ibd"/>
 </param>
-<repeat name="repeatpixel">
+<conditional name="pixel_conditional">
-<param name="plusminusinDalton" value="0.25"/>
+<param name="pixel_type" value="single_pixel"/>
-<param name="inputx" value="3"/>
+<repeat name="repeatpixel">
-<param name="inputy" value="3"/>
+<param name="plusminusinDalton" value="0.25"/>
-<repeat name="zoomedplot">
+<param name="inputx" value="3"/>
-<param name="xlimmin" value="550"/>
+<param name="inputy" value="3"/>
-<param name="xlimmax" value="555"/>
+<repeat name="zoomedplot">
-</repeat>
+<param name="xlimmin" value="550"/>
-<repeat name="zoomedplot">
+<param name="xlimmax" value="555"/>
-<param name="xlimmin" value="750"/>
+</repeat>
-<param name="xlimmax" value="800"/>
+<repeat name="zoomedplot">
-</repeat>
+<param name="xlimmin" value="750"/>
-<repeat name="zoomedplot">
+<param name="xlimmax" value="800"/>
-<param name="xlimmin" value="400"/>
+</repeat>
-<param name="xlimmax" value="420"/>
+<repeat name="zoomedplot">
-</repeat>
+<param name="xlimmin" value="400"/>
-</repeat>
+<param name="xlimmax" value="420"/>
-<repeat name="repeatpixel">
+</repeat>
-<param name="plusminusinDalton" value="0.25"/>
+</repeat>
-<param name="inputx" value="2"/>
+<repeat name="repeatpixel">
-<param name="inputy" value="2"/>
+<param name="plusminusinDalton" value="0.25"/>
-</repeat>
+<param name="inputx" value="2"/>
-<repeat name="repeatpixel">
+<param name="inputy" value="2"/>
-<param name="plusminusinDalton" value="0.25"/>
+</repeat>
-<param name="inputx" value="1"/>
+<repeat name="repeatpixel">
-<param name="inputy" value="1"/>
+<param name="plusminusinDalton" value="0.25"/>
-</repeat>
+<param name="inputx" value="1"/>
+<param name="inputy" value="1"/>
+</repeat>
+</conditional>
 <output name="plots" file="Plot_imzml.pdf" compare="sim_size" delta="20000"/>
-<output name="tabularmatrix" file="Matrix_imzml.txt"/>
 </test>
 <test>
 <param name="infile" value="" ftype="analyze75">
 <composite_data value="Analyze75.hdr"/>
 <composite_data value="Analyze75.img"/>
 <composite_data value="Analyze75.t2m"/>
 </param>
-<repeat name="repeatpixel">
+<conditional name="pixel_conditional">
-<param name="plusminusinDalton" value="0.25"/>
+<param name="pixel_type" value="single_pixel"/>
-<param name="inputx" value="5"/>
+<repeat name="repeatpixel">
-<param name="inputy" value="2"/>
+<param name="plusminusinDalton" value="0.25"/>
-<repeat name="zoomedplot">
+<param name="inputx" value="5"/>
-<param name="xlimmin" value="840"/>
+<param name="inputy" value="2"/>
-<param name="xlimmax" value="850"/>
+<repeat name="zoomedplot">
-</repeat>
+<param name="xlimmin" value="840"/>
-</repeat>
+<param name="xlimmax" value="850"/>
-<repeat name="repeatpixel">
+</repeat>
-<param name="plusminusinDalton" value="0.25"/>
+</repeat>
-<param name="inputx" value="2"/>
+<repeat name="repeatpixel">
-<param name="inputy" value="2"/>
+<param name="plusminusinDalton" value="0.25"/>
-</repeat>
+<param name="inputx" value="2"/>
+<param name="inputy" value="2"/>
+</repeat>
+</conditional>
 <output name="plots" file="Plot_analyze75.pdf" compare="sim_size" delta="20000"/>
-<output name="tabularmatrix" file="Matrix_analyze75.txt"/>
-</test>
-<test>
-<param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>
-<repeat name="repeatpixel">
-<param name="plusminusinDalton" value="0.25"/>
-<param name="inputx" value="2"/>
-<param name="inputy" value="2"/>
-<repeat name="zoomedplot">
-<param name="xlimmin" value="222"/>
-<param name="xlimmax" value="244"/>
-</repeat>
-</repeat>
-<output name="plots" file="Plot_rdata.pdf" compare="sim_size" delta="20000"/>
-<output name="tabularmatrix" file="Matrix_rdata.txt"/>
 </test>
 <test>
-<param name="infile" value="LM8_file16.rdata" ftype="rdata"/>
+<param name="infile" value="123_combined.rdata" ftype="rdata"/>
+<conditional name="pixel_conditional">
+<param name="pixel_type" value="sample_pixel"/>
+<repeat name="zoomed_sample">
+<param name="xlimmin" value="350"/>
+<param name="xlimmax" value="360"/>
+</repeat>
+</conditional>
+<output name="plots" file="Plot_rdata.pdf" compare="sim_size" delta="20000"/>
+</test>
+<test>
+<param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
 <param name="plusminusinDalton" value="0.1"/>
 <param name="inputx" value="1"/>
 <param name="inputy" value="1"/>
 <repeat name="repeatpixel">
 <param name="plusminusinDalton" value="0.25"/>
 <repeat name="zoomedplot">
 <param name="xlimmin" value="1000"/>
 <param name="xlimmax" value="1050"/>
 </repeat>
 </repeat>
-<output name="plots" file="Plot_LM8_file16.pdf" compare="sim_size" delta="20000"/>
+<output name="plots" file="Plot_empty_spectra.pdf" compare="sim_size" delta="20000"/>
-<output name="tabularmatrix" file="Matrix_LM8.txt"/>
 </test>
 </tests>
 <help><![CDATA[
-Returns a full mass-spectrum plot and peaklist output with masses and intensities for the chosen pixel. Input needs the x and the y coordinates of the pixel of interest.
+Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
-Additionally zoom into mass-spectra plots is possible by providing the minimum and maximum mz value to define the limits of the plot.
-To have a visual control that the right pixel was chosen, a heatmap of a mass in Dalton which can be specified will be plotted and two intersecting lines will show where the chosen pixel is located in the ion image.
+This tool uses the Cardinal plot function to generate (zoomed in) mass spectra plots of mass-spectrometry imaging data.
 Input data: 3 types of input data can be used:
-- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_
+- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
-The output of this tool contains a heatmap of the mass of interest with two lines intersecting at the pixel of interest. Then the full mass-spectrum plot is obtained and if chosen also several zoomed in mass spectra. A peaklist with masses and intensities for this pixel is exported as tabular file.
+Options:
+- "single pixel": Returns a full mass-spectrum plot for one pixel, which is defined by its x- and y-coordinates
+- Enter the x and y coordinates of your pixel of interest
+- To have a visual control for the selected pixel, a heatmap of a mass of interest will be drawn. Two intersecting lines will show the pixel location. This procedure requires an mass of interest together with a mass range and for the lines the colour and type.
+- Additionally zoom into mass-spectra plots is possible by providing the minimum and maximum mass value to define the limits of the plot
+- "All pixels of a sample": Returns a full average mass-spectrum plot with different colours for each subfile
+- This option only works on files that have previosly been combined in the combine tool
+- Additionally zoom into mass-spectra plots is possible by providing the minimum and maximum mass value to define the limits of the plot
+Output:
+- Pdf with the selected mass-spectra plots and additional control plots
+Tip:
+- Corresponding peaklists with masses and their intensities can be obtained with the filtering tool option "ranges for x and y"
 ]]>
 </help>
 <citations>
 <citation type="doi">10.1093/bioinformatics/btv146</citation>

Mercurial > repos > galaxyp > msi_spectra_plot

comparison msi_spectra_plots.xml @ 2:ea4f1c516368 draft