cardinal_filtering: filtering.xml comparison

comparison filtering.xml @ 6:97fdb0ce4dd3 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"

author	galaxyp
date	Wed, 25 Mar 2020 09:24:18 +0000
parents	b045ba419ac6
children	5aaea231da6b

comparison

equal deleted inserted replaced

-:44dfff9c268f
+:97fdb0ce4dd3
-<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.3">
+<tool id="cardinal_filtering" name="MSI filtering" version="2.4.0.0">
 <description>tool for filtering mass spectrometry imaging data</description>
 <macros>
 <import>macros.xml</import>
 </macros>
-<expand macro="requirements">
+<requirements>
+<requirement type="package" version="2.4.0">bioconductor-cardinal</requirement>
+<requirement type="package" version="3.6.1">r-base</requirement>
 <requirement type="package" version="2.3">r-gridextra</requirement>
-<requirement type="package" version="3.0">r-ggplot2</requirement>
+<requirement type="package" version="3.2.1">r-ggplot2</requirement>
-</expand>
+</requirements>
 <expand macro="print_version"/>
 <command detect_errors="exit_code">
 <![CDATA[
 @INPUT_LINKING@
 cat '${MSI_subsetting}' &&
 Rscript '${MSI_subsetting}' &&
+mkdir $outfile_imzml.files_path &&
-#if str($imzml_output) == "imzml_format":
+mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
-mkdir $outfile_imzml.files_path &&
+mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
-mv ./out.imzML "${os.path.join($outfile_imzml.files_path, 'imzml')}" | true &&
-mv ./out.ibd "${os.path.join($outfile_imzml.files_path, 'ibd')}" | true &&
-#end if
 echo "imzML file:" > $outfile_imzml &&
 ls -l "$outfile_imzml.files_path" >> $outfile_imzml
 ]]>
 </command>
 library(Cardinal)
 library(ggplot2)
 library(gridExtra)
-@READING_MSIDATA@
+## function to read RData files independent of filename
+loadRData <- function(fileName){
+load(fileName)
+get(ls()[ls() != "fileName"])
+}
+#if $infile.ext == 'imzml'
+#if str($processed_cond.processed_file) == "processed":
+msidata <- readImzML('infile', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE)
+centroided(msidata) = $centroids
+#else
+msidata <- readImzML('infile', attach.only=TRUE)
+centroided(msidata) = $centroids
+#end if
+#elif $infile.ext == 'analyze75'
+msidata = readAnalyze('infile', attach.only=TRUE)
+centroided(msidata) = $centroids
+#else
+msidata = loadRData('infile.RData')
+msidata = as(msidata, "MSImagingExperiment")
+#end if
 ########################### QC numbers ########################
 ## Number of features (m/z)
-maxfeatures = length(features(msidata))
+maxfeatures = nrow(msidata)
 ## Range m/z
 minmz = round(min(mz(msidata)), digits=2)
 maxmz = round(max(mz(msidata)), digits=2)
 ## Number of spectra (pixels)
-pixelcount = length(pixels(msidata))
+pixelcount = ncol(msidata)
 ## Range x coordinates
-minimumx = min(coord(msidata)[,1])
+minimumx = min(coord(msidata)\$x)
-maximumx = max(coord(msidata)[,1])
+maximumx = max(coord(msidata)\$x)
 ## Range y coordinates
-minimumy = min(coord(msidata)[,2])
+minimumy = min(coord(msidata)\$y)
-maximumy = max(coord(msidata)[,2])
+maximumy = max(coord(msidata)\$y)
 ## Store features for QC plot
 featuresinfile = mz(msidata)
-all_df = cbind(coord(msidata)[,1:2], rep("removed pixels", times=ncol(msidata)))
+all_df = data.frame(coord(msidata)\$x, coord(msidata)\$y, rep("removed pixels", times=ncol(msidata)))
-colnames(all_df)[3] = "annotation"
+colnames(all_df) = c("x", "y", "annotation")
 ## Next steps will only run if there are more than 0 pixels/features in the file
 if (ncol(msidata)>0 & nrow(msidata) >0)
 {
 }
 },
 error=function(cond) {
 ## in case all coordinates were outside the dataset leading to zero pixels, tool is stopped to avoid continuing with wrong data
 message("Error during pixel filtering")
-message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, columns with coordinates contain empty fields or letters, all coordinates were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool)")
+message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, columns with coordinates contain empty fields or letters, all coordinates were outside the range of the dataset - this can be checked with the 'MSI qualitycontrol' tool")
 stop(call.=FALSE)
 }
 )
 ## QC values:
 ############################# QC data #####################################
 ## dataframe for QC of pixel distribution
-remaining_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata)))
+remaining_df = data.frame(as.numeric(coord(msidata)\$x), as.numeric(coord(msidata)\$y), rep("remaining pixels", times=ncol(msidata)))
-colnames(remaining_df)[3] = "annotation"
+colnames(remaining_df) = c("x", "y", "annotation")
 position_df = rbind(all_df, remaining_df)
 position_df[row.names(unique(position_df[,c("x", "y")])),]
 position_df\$annotation = factor(position_df\$annotation)
 gc()
 }else{
 },
 error=function(cond) {
 ## in case all provided m/z values were outside the m/z range
 ## tool is stopped to avoid continuing with wrong data
 message("Error during m/z filtering")
-message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, column with m/z features contains empty fields or letters, all m/z features s were outside the range of the dataset  - this can be checked with the 'MSI qualitycontrol' tool) or did not match any m/z feature of the dataset (see help section for more information on that)")
+message("Possible problems: Forgot to set 'Tabular file contains a header line' = Yes, wrong columns selected, column with m/z features contains empty fields or letters, all m/z features s were outside the range of the dataset  (this can be checked with the 'MSI qualitycontrol' tool) or did not match any m/z feature of the dataset (see help section for more information on that)")
 stop(call.=FALSE)
 }
 )
 #if str($features_cond.units_removal) == "ppm":
 plusminus = masses * $features_cond.removal_plusminus/1000000
 #end if
 current_mass = which(c(mz(msidata) <= masses + plusminus & mz(msidata) >= masses - plusminus))
 mass_to_remove = append(mass_to_remove, current_mass)}
-msidata= msidata[-mass_to_remove, ]
+mass_to_keep = setdiff(1:nrow(msidata),mass_to_remove)
-validmz = numberfeatures - nrow(msidata)
+msidata= msidata[mass_to_keep, ]
+validmz = maxfeatures - nrow(msidata)
 ## does not throw error when processed file has no features left, therefore create error to avoid continuing with wrong data
 if (nrow(msidata) == 0)
 {
 stop(call.=FALSE)
 }
 }
 )
 ######################## No m/z filtering ##############################
 #elif str($features_cond.features_filtering) == "none":
 print("no feature filtering")
 gc()
 #################### QC numbers #######################
 ## Number of features (m/z)
-maxfeatures2 = length(features(msidata))
+maxfeatures2 = nrow(msidata)
 ## Range m/z
 minmz2 = round(min(mz(msidata)), digits=2)
 maxmz2 = round(max(mz(msidata)), digits=2)
 ## Number of spectra (pixels)
-pixelcount2 = length(pixels(msidata))
+pixelcount2 = ncol(msidata)
 ## Range x coordinates
-minimumx2 = min(coord(msidata)[,1])
+minimumx2 = min(coord(msidata)\$x)
-maximumx2 = max(coord(msidata)[,1])
+maximumx2 = max(coord(msidata)\$x)
 ## Range y coordinates
-minimumy2 = min(coord(msidata)[,2])
+minimumy2 = min(coord(msidata)\$y)
-maximumy2 = max(coord(msidata)[,2])
+maximumy2 = max(coord(msidata)\$y)
 properties = c("Number of m/z features",
 "Range of m/z values",
 "Number of pixels",
 "Range of x coordinates",
 ########################### PDF QC and MSI output ###########################
 pdf("filtertool_QC.pdf", fonts = "Times", pointsize = 12)
 plot(0,type='n',axes=FALSE,ann=FALSE)
-title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.display_name"))
+title(main=paste0("Qualitycontrol of filtering tool for file: \n\n", "$infile.element_identifier"))
 grid.table(property_df, rows= NULL)
 ## QC report only when pixels/features are left
 if (ncol(msidata)>0 & nrow(msidata) >0)
 {
 geom_tile(height = 1, width=1)+
 coord_fixed()+
 ggtitle("Spatial orientation of filtered pixels")+
 theme_bw()+
 theme(plot.title = element_text(hjust = 0.5))+
-theme(legend.position="bottom",legend.direction="vertical")
+theme(legend.position="bottom",legend.direction="vertical")+
+guides(fill=guide_legend(ncol=5,byrow=TRUE))
 print(pixel_image)
-### plot features which are removed
-hist(mz(msidata), xlab="m/z", main="Kept m/z values")
+### visual mz feature control
-#if str($features_cond.features_filtering) == "none":
-print("no difference histogram as no m/z filtering took place")
+kept_df = data.frame(mz(msidata), rep("remaining m/z", nrow(msidata)))
-#else:
+colnames(kept_df) = c("mz", "legend")
-if (isTRUE(all.equal(featuresinfile, mz(msidata)))){
-print("No difference in m/z values before and after filtering, no histogram drawn")
+mz_removed = setdiff(featuresinfile, mz(msidata))
-}else{
+removed_df = data.frame(mz_removed, rep("removed m/z", length(mz_removed)))
-hist(setdiff(featuresinfile, mz(msidata)), xlab="m/z", main="Removed m/z values")}
+colnames(removed_df) = c("mz", "legend")
-#end if
+histogram_df = rbind(removed_df,kept_df)
+histogram_mz= ggplot(histogram_df, aes(x=mz, fill=legend)) +
+geom_histogram()+ theme_bw()+
+theme(plot.title = element_text(hjust = 0.5))+
+theme(legend.position="bottom",legend.direction="vertical")+
+labs(title="Overview of filtered m/z", x="m/z", y = "count") +
+guides(fill=guide_legend(ncol=5,byrow=TRUE))
+print(histogram_mz)
 dev.off()
 ## save msidata as imzML file, will only work if there is at least 1 m/z left
-#if str($imzml_output) == "imzml_format":
 if (maxfeatures2 > 0){
 ## make sure that coordinates are integers
 coord(msidata)\$y = as.integer(coord(msidata)\$y)
 coord(msidata)\$x = as.integer(coord(msidata)\$x)
 writeImzML(msidata, "out")}
-#elif str($imzml_output) == "rdata_format":
-## save msidata as Rfile
-iData(msidata) = iData(msidata)[]
-save(msidata, file="$outfile_rdata")
-#end if
 }else{
 print("Inputfile or filtered file has no intensities > 0")
 dev.off()
 <option value="ppm" selected="True">ppm</option>
 <option value="Da">Da</option>
 </param>
 </when>
 </conditional>
-<param name="imzml_output" type="select" display = "radio" optional = "False"
-label="Output format" help= "Choose the output format">
-<option value="imzml_format" >imzML</option>
-<option value="rdata_format" selected="True" >RData</option>
-</param>
 </inputs>
 <outputs>
-<data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML">
+<data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML"/>
-<filter>imzml_output =='imzml_format'</filter>
-</data>
-<data format="rdata" name="outfile_rdata" label="${tool.name} on ${on_string}: RData">
-<filter>imzml_output == 'rdata_format'</filter>
-</data>
 <data format="pdf" name="QC_overview" from_work_dir="filtertool_QC.pdf" label = "${tool.name} on ${on_string}: QC"/>
 </outputs>
 <tests>
 <test>
 <expand macro="infile_imzml"/>
 <param name="min_y_range" value="2"/>
 <param name="max_y_range" value="2"/>
 <param name="features_filtering" value="features_range"/>
 <param name="min_mz" value="350"/>
 <param name="max_mz" value="500"/>
-<param name="imzml_output" value="imzml_format"/>
 <output name="QC_overview" file="imzml_filtered3.pdf" compare="sim_size"/>
 <output name="outfile_imzml" ftype="imzml" file="out3.imzml.txt" compare="sim_size">
-<extra_files type="file" file="out3.imzml" name="imzml" lines_diff="4"/>
+<extra_files type="file" file="out3.imzml" name="imzml" lines_diff="6"/>
 <extra_files type="file" file="out3.ibd" name="ibd" compare="sim_size"/>
 </output>
 </test>
 <test>
 <expand macro="infile_imzml"/>
 <param name="pixel_filtering" value="two_columns"/>
 <param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/>
 <param name="column_x" value="1"/>
 <param name="column_y" value="3"/>
-<param name="imzml_output" value="imzml_format"/>
 <output name="QC_overview" file="imzml_filtered4.pdf" compare="sim_size"/>
 <output name="outfile_imzml" ftype="imzml" file="out4.imzml.txt" compare="sim_size">
-<extra_files type="file" file="out4.imzml" name="imzml" lines_diff="4"/>
+<extra_files type="file" file="out4.imzml" name="imzml" lines_diff="6"/>
 <extra_files type="file" file="out4.ibd" name="ibd" compare="sim_size"/>
 </output>
 </test>
 <test>
 <expand macro="infile_imzml"/>
 <param name="max_y_range" value="20"/>
 <param name="features_filtering" value="features_list"/>
 <param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>
 <param name="feature_column" value="1"/>
 <param name="feature_header" value="0"/>
-<param name="imzml_output" value="imzml_format"/>
 <output name="QC_overview" file="imzml_filtered5.pdf" compare="sim_size"/>
 <output name="outfile_imzml" ftype="imzml" file="out5.imzml.txt" compare="sim_size">
-<extra_files type="file" file="out5.imzml" name="imzml" lines_diff="4"/>
+<extra_files type="file" file="out5.imzml" name="imzml" lines_diff="6"/>
 <extra_files type="file" file="out5.ibd" name="ibd" compare="sim_size"/>
 </output>
 </test>
 <test>
 <expand macro="infile_analyze75"/>
-<param name="imzml_output" value="imzml_format"/>
 <output name="QC_overview" file="analyze75_filtered2.pdf" compare="sim_size"/>
 <output name="outfile_imzml" ftype="imzml" file="out6.imzml.txt" compare="sim_size">
-<extra_files type="file" file="out6.imzml" name="imzml" lines_diff="4"/>
+<extra_files type="file" file="out6.imzml" name="imzml" lines_diff="6"/>
 <extra_files type="file" file="out6.ibd" name="ibd" compare="sim_size"/>
 </output>
 </test>
 <test>
 <param name="infile" value="preprocessed.RData" ftype="rdata"/>
-<conditional name="outputs">
-<param name="outputs_select" value="no_quality_control"/>
-</conditional>
-<param name="imzml_output" value="imzml_format"/>
 <output name="QC_overview" file="rdata_notfiltered.pdf" compare="sim_size" />
 <output name="outfile_imzml" ftype="imzml" file="out7.imzml.txt" compare="sim_size">
-<extra_files type="file" file="out7.imzml" name="imzml" lines_diff="4"/>
+<extra_files type="file" file="out7.imzml" name="imzml" lines_diff="6"/>
 <extra_files type="file" file="out7.ibd" name="ibd" compare="sim_size"/>
+</output>
+</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="pixel_filtering" value="two_columns"/>
+<param name="annotation_file" ftype="tabular" value="inputpixels_2column.tabular"/>
+<param name="column_x" value="1"/>
+<param name="column_y" value="3"/>
+<param name="features_filtering" value="remove_features"/>
+<param name="mz_tabular" ftype="tabular" value = "featuresofinterest5.tabular"/>
+<param name="feature_column" value="1"/>
+<param name="feature_header" value="0"/>
+<param name="removal_plusminus" value="100"/>
+<param name="units_removal" value="ppm"/>
+<output name="QC_overview" file="imzml_filtered8.pdf" compare="sim_size"/>
+<output name="outfile_imzml" ftype="imzml" file="out8.imzml.txt" compare="sim_size">
+<extra_files type="file" file="out8.imzml" name="imzml" lines_diff="6"/>
+<extra_files type="file" file="out8.ibd" name="ibd" compare="sim_size"/>
 </output>
 </test>
 </tests>
 <help>
 <![CDATA[
 - An error occurs if the input for filtering (tabular file or mz-range) contains not a single m/z feature that occurs in the dataset
 - m/z feature removing:
-- Perturbing m/z features such as matrix contaminants can be removed by specifying their m/z value in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed
+- Perturbing m/z features such as matrix contaminants, tryptic peptides and internal calibrants can be removed by specifying their m/z value in a tabular file, optionally with a half window size in ppm or m/z for the window in which peaks should be removed
 **Tips**
 - m/z feautre filtering with a tabular file:
 - In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy might be different from 'tabular' - datatype can be changed by pressing the pen button of the dataset (edit attributes)
 **Output**
-- MSI data as imzML file or .RData (can be read with the Cardinal package in R)
+- MSI data as (continuous) imzML file
 - pdf with heatmap showing the pixels that are removed and kept as well as histograms of kept and removed m/z
 ]]>
 </help>

Mercurial > repos > galaxyp > cardinal_filtering

comparison filtering.xml @ 6:97fdb0ce4dd3 draft