cardinal_mz_images: mz_images.xml comparison

comparison 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

comparison

equal deleted inserted replaced

-:25b83cbd596a
+:5e6f8fb2df07
-<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>
 <macros>
 <import>macros.xml</import>
 </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[
 @INPUT_LINKING@
 cat '${MSI_heatmaps}' &&
 ################################# load libraries and read file #################
 library(Cardinal)
 library(gridExtra)
-library(lattice)
+##library(lattice)
-@READING_MSIDATA@
+@READING_MSIDATA_FULLY_COMPATIBLE@
 @DATA_PROPERTIES@
 ##################################### read and filter input m/z ##############
 grid.table(property_df, rows= NULL)
 ############################# 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
+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=$colorscale, ylim= c(maximumy,minimumy)))}
-#if str($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")
-#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))
+par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg
-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")
+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="$normalize_image"))
 dev.off()
 #end if
 ## optional overlay all input m/z in one image
 #if str($overlay_cond.overlay_selection) == "yes_overlay":
 #set $color_string = ','.join(['"%s"' % $color.feature_color for $color in $overlay_cond.colours])
 colourvector = c($color_string)
+par(mar=c(0,0,0,0), oma=c(0,0,0,1))## margin for image legend
-image(msidata, mz=inputmz,
+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))))
 #end if
 } else {print("The input m/z were invalid")}
 dev.off()
 }else{
 <inputs>
 <expand macro="reading_msidata"/>
 <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>
 <option value="histogram">histogram</option>
 </param>
 <param name="image_smoothing" type="select" label="Image smoothing" help="The 'gaussian' smoothing method smooths images with a simple gaussian kernel. The 'adaptive' method uses bilateral filtering to preserve edges">
 <option value="none" selected="True">none</option>
 <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"
+<param name="normalize_image" type="boolean" truevalue="linear" falsevalue="none" label="Linear normalization of image"/>
-label="Standard image" help="No: lattice function is used to display 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">
 <option value="no_overlay" selected="True">no</option>
 <option value="yes_overlay">yes</option>
 <add value="#" />
 </valid>
 </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>
 <outputs>
 <data format="pdf" name="plots" from_work_dir="heatmaps.pdf" label="${tool.name} on ${on_string}: results"/>
 <param name="plusminus_dalton" value="0.25"/>
 <param name="filename" value="Testfile_imzml"/>
 <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>
 <expand macro="infile_analyze75"/>
 <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>
 <param name="mz_column" value="1"/>
 <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"/>
 <param name="svg_pixelimage" value="True"/>
 <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/>
 <param name="mz_column" value="1"/>
 <param name="name_column" value="2"/>
 <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>
 <test>
 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
 <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/>
 <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
 ]]>
 </help>

Mercurial > repos > galaxyp > cardinal_mz_images

comparison mz_images.xml @ 7:5e6f8fb2df07 draft