Mercurial > repos > galaxyp > cardinal_mz_images
diff mz_images.xml @ 7:5e6f8fb2df07 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f986c51abe33c7f622d429a3c4a79ee24b33c1f3"
| author | galaxyp |
|---|---|
| date | Thu, 23 Apr 2020 08:08:28 -0400 |
| parents | 773a24b240e1 |
| children | 08ebd8da780c |
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--- a/mz_images.xml Wed Mar 25 05:31:15 2020 -0400 +++ b/mz_images.xml Thu Apr 23 08:08:28 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.2"> +<tool id="cardinal_mz_images" name="MSI mz images" version="@VERSION@.0"> <description> mass spectrometry imaging m/z heatmaps </description> @@ -7,7 +7,6 @@ </macros> <expand macro="requirements"> <requirement type="package" version="2.3">r-gridextra</requirement> - <requirement type="package" version="0.20_35">r-lattice</requirement> </expand> <command detect_errors="aggressive"> <![CDATA[ @@ -23,9 +22,9 @@ library(Cardinal) library(gridExtra) -library(lattice) +##library(lattice) -@READING_MSIDATA@ +@READING_MSIDATA_FULLY_COMPATIBLE@ @DATA_PROPERTIES@ @@ -59,52 +58,26 @@ ############################# II) images #################################### ### only plot images when file has features and pixels: - +par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend if (ncol(msidata)>0 & nrow(msidata) >0){ if (length(inputmz) != 0){ for (mass in 1:length(inputmz)){ - ###standard image - - #if str($image_type) == "standard_image": - print("standard image") - - print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", - smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey,ylim= c(maximumy+0.2*maximumy,minimumy-1), - main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} - - - ###lattice image - - #elif str($image_type) == "lattice_image": - print("lattice image") + print(image(msidata, mz=inputmz[mass],plusminus = $plusminus_dalton, normalize.image="$normalize_image", contrast.enhance = "$image_contrast", + smooth.image = "$image_smoothing", strip=$strip, colorkey=$colorkey, colorscale=$colorscale, ylim= c(maximumy,minimumy)))} - #if str($strip) =="TRUE": - - print(image(msidata, mz=inputmz[mass], strip = strip.custom(bg="lightgrey", par.strip.text=list(col="black", cex=.9)), - lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", - colorkey=$colorkey,ylim=c(maximumy+0.2*maximumy,minimumy-1), - main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} - - #elif str($strip) =="FALSE": - - print(image(msidata, mz=inputmz[mass], strip = $strip, - lattice=TRUE, plusminus = $plusminus_dalton, contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", - colorkey=$colorkey, - main= paste0(inputnames[mass], " (", round(inputmz[mass], digits = 2)," ± ", $plusminus_dalton, " Da)")))} - - #end if - - #end if ## optional svg output with original coordinates #if $svg_pixelimage: print("svg pixel image") ## reverse y axis for svg output = correct order and nice svg image coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1 + ## works only with MSImageSet as expected + msidata = as(msidata, "MSImageSet") + svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy) - par(mar=c(0,0,0,0)) - image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton,colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing") + par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg + print(image(msidata, mz = inputmz[1],strip=FALSE, plusminus = $plusminus_dalton, colorscale=$colorscale, colorkey = FALSE,axes=FALSE, xlab=NA, ylab=NA,contrast.enhance = "$image_contrast", smooth.image = "$image_smoothing", normalize.image="$normalize_image")) dev.off() #end if @@ -113,19 +86,20 @@ #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours]) colourvector = c($color_string) - - image(msidata, mz=inputmz, + par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend + print(image(msidata, mz=inputmz, plusminus = $plusminus_dalton, col=colourvector, contrast.enhance = "$image_contrast", - normalize.image="linear", + normalize.image="$normalize_image", smooth.image = "$image_smoothing", superpose=TRUE, main="overlay of all m/z", - ylim= c(maximumy+0.2*maximumy,minimumy-1)) + key=FALSE, + ylim= c(maximumy,minimumy))) - legend("topright", + legend("$overlay_cond.legend_position", fill=colourvector, - legend=as.numeric(sort(as.character(inputmz)))) + legend=as.numeric(sort(as.character(inputmz)))) #end if } else {print("The input m/z were invalid")} @@ -143,7 +117,7 @@ <expand macro="pdf_filename"/> <expand macro="reading_2_column_mz_tabular"/> - + <param name="plusminus_dalton" value="0.25" type="float" label="m/z range" help="average of the m/z window will be computed"/> <param name="image_contrast" type="select" label="Contrast enhancement" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots"> <option value="none" selected="True">none</option> <option value="suppression">suppression</option> @@ -154,11 +128,15 @@ <option value="gaussian">gaussian</option> <option value="adaptive">adaptive</option> </param> - <param name="plusminus_dalton" value="0.25" type="float" label="M/z range" help="plusminus m/z window"/> + <param name="colorscale" type="select" display="radio" label="Colorscale"> + <option value="viridis" selected="True">viridis</option> + <option value="magma">magma</option> + <option value="plasma">plasma</option> + <option value="inferno">inferno</option> + </param> <param name="strip" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display m/z value in plot"/> <param name="colorkey" type="boolean" checked="True" truevalue="TRUE" falsevalue="FALSE" label="Display colorkey in plot"/> - <param name="image_type" type="boolean" checked="True" truevalue="standard_image" falsevalue="lattice_image" - label="Standard image" help="No: lattice function is used to display image"/> + <param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/> <param name="svg_pixelimage" type="boolean" label="Export first valid m/z from tabular file as SVG"/> <conditional name="overlay_cond"> <param name="overlay_selection" type="select" label="Overlay image"> @@ -176,6 +154,16 @@ </sanitizer> </param> </repeat> + <param name="legend_position" type="select" display="radio" label="Position of legend"> + <option value="topright" selected="True">topright</option> + <option value="top">top</option> + <option value="topleft">topleft</option> + <option value="left">left</option> + <option value="bottomleft">bottomleft</option> + <option value="bottom">bottom</option> + <option value="bottomright">bottomright</option> + <option value="right">right</option> + </param> </when> </conditional> </inputs> @@ -196,7 +184,6 @@ <param name="image_contrast" value="histogram"/> <param name="strip" value="True"/> <param name="colorkey" value="True"/> - <param name="image_type" value="lattice_image"/> <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/> </test> <test> @@ -206,6 +193,7 @@ <param name="name_column" value="1"/> <param name="plusminus_dalton" value="0.5"/> <param name="filename" value="Testfile_analyze75"/> + <param name="colorscale" value="magma"/> <param name="image_smoothing" value="gaussian"/> <param name="strip" value="False"/> <param name="colorkey" value="True"/> @@ -221,7 +209,6 @@ <param name="plusminus_dalton" value="0.5"/> <param name="strip" value="True"/> <param name="colorkey" value="True"/> - <param name="image_type" value="lattice_image"/> <param name="filename" value="Testfile_rdata"/> <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/> </test> @@ -231,35 +218,59 @@ <param name="mz_column" value="1"/> <param name="name_column" value="1"/> <param name="plusminus_dalton" value="0.5"/> + <param name="colorscale" value="plasma"/> <param name="strip" value="True"/> <param name="colorkey" value="False"/> <param name="filename" value="Testfile_rdata"/> <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/> </test> + <test> + <expand macro="processed_infile_imzml"/> + <conditional name="processed_cond"> + <param name="processed_file" value="processed"/> + <param name="accuracy" value="100"/> + <param name="units" value="ppm"/> + </conditional> + <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> + <param name="mz_column" value="1"/> + <param name="name_column" value="2"/> + <conditional name="overlay_cond"> + <param name="overlay_selection" value="yes_overlay"/> + <repeat name="colours"> + <param name="feature_color" value="#ff00ff"/> + </repeat> + <repeat name="colours"> + <param name="feature_color" value="#1f497d"/> + </repeat> + <repeat name="colours"> + <param name="feature_color" value="#00b050"/> + </repeat> + <param name="legend_position" value="topleft"/> + </conditional> + <output name="plots" file="Heatmaps_processed.pdf" ftype="pdf" compare="sim_size"/> + </test> </tests> <help><![CDATA[ - @CARDINAL_DESCRIPTION@ ----- -This tool uses the Cardinal image function to plot the intensity distribution of m/z feature of mass spectrometry imaging data. +This tool uses the Cardinal image function to plot the intensity distribution of m/z features of mass spectrometry imaging data. @MSIDATA_INPUT_DESCRIPTION@ @MZ_2COLS_TABULAR_INPUT_DESCRIPTION@ + **Tips** - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy must be tabular otherwise file will not appear in selection window (if Galaxy auto-detection was wrong, datatype can be changed by pressing the pen button (edit attributes)) -- No heatmaps are plotted when the input mass spectrometry imaging file has no intensities > 0 or all chosen m/z features are not present in the MSI dataset - The contrast enhance and image smoothing functions require a certain number (about 2%) of m/z features with intensities > 0 across all spectra -- The standard image function should work for all files while the lattice function works not perfectly on every file **Output** -- Pdf with the heatmap images +- Single Pdf with the heatmap images - optional: svg file with the heatmap of the first valid m/z in the tabular file