Mercurial > repos > galaxyp > cardinal_combine
changeset 6:bb1ac6b47a6c draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
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--- a/combine.xml Fri Dec 13 13:54:23 2019 -0500 +++ b/combine.xml Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="cardinal_combine" name="MSI combine" version="2.2.6.0"> +<tool id="cardinal_combine" name="MSI combine" version="2.2.6.1"> <description> combine several mass spectrometry imaging datasets into one </description> @@ -44,6 +44,7 @@ </command> <configfiles> <configfile name="msi_combine"><![CDATA[ + #import re ################ 1) load libraries and do preparations ################# @@ -86,7 +87,7 @@ #if $infile.ext == 'imzml' #if str($processed_cond.processed_file) == "processed": - msidata_$i <- readImzML('infile_${i}', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE, as = c("MSImageSet")) + msidata_$i <- readImzML('infile_${i}', resolution=$processed_cond.accuracy, units = "$processed_cond.units", attach.only=TRUE, as = c("MSImageSet")) centroided(msidata_$i) = $centroids #else msidata_$i <- readImzML('infile_${i}', attach.only=TRUE, as = c("MSImageSet")) @@ -235,7 +236,7 @@ #end for -######################### 6a) combination same mz axis ################### +######################### 6b) combination same mz axis ################### #if str( $combine_conditional.combine_method ) == 'automatic_combine': print("automatic combine") @@ -294,12 +295,7 @@ ## save msidata as imzML file MALDIquant MALDIquantForeign::exportImzMl(filtered_dataset, file="out.imzML", processed=TRUE, coordinates=coordinates_matrix) - ## create x,y,sample_name dataframe for QC pdf - ## position_df = unique_coordinates ### ! anders - ## colnames(position_df)[3] = "sample_name" - ##coordinates_combined = coordinates_combined[pixelsofinterest,] ###! anders coordinates_combined = unique_coordinates -##TODO: hier aufräumen kann alles weg?! #end if @@ -323,7 +319,6 @@ guides(fill=guide_legend(ncol=4,byrow=TRUE)) coord_labels = aggregate(cbind(x,y)~sample_name, data=coordinates_combined[,1:3], mean) coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name) - print(combine_plot) #if str($annotation_cond.annotation_tabular) == 'annotation' @@ -431,7 +426,7 @@ <output name="pixel_annotations" file="123_annotation_output.tabular"/> <output name="QC_overview" file="123_combined_QC.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="123_combined.imzml.txt" compare="sim_size"> - <extra_files type="file" file="123_combined.imzml" name="imzml" lines_diff="4"/> + <extra_files type="file" file="123_combined.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="123_combined.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -447,7 +442,7 @@ <output name="pixel_annotations" file="picked.tabular"/> <output name="QC_overview" file="picked_QC.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="picked.imzml.txt" compare="sim_size"> - <extra_files type="file" file="picked.imzml" name="imzml" lines_diff="6"/> + <extra_files type="file" file="picked.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="picked.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -461,7 +456,7 @@ <output name="QC_overview" file="123_combined_auto.pdf" compare="sim_size"/> <output name="pixel_annotations" file="123_combined_auto.tabular"/> <output name="outfile_imzml" ftype="imzml" file="123_combined_auto.imzml.txt" compare="sim_size"> - <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="4"/> + <extra_files type="file" file="123_combined_auto.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="123_combined_auto.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -477,7 +472,7 @@ <output name="pixel_annotations" file="12_annotation_output.tabular"/> <output name="QC_overview" file="12_combined_QC.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="12_combined.imzml.txt" compare="sim_size"> - <extra_files type="file" file="12_combined.imzml" name="imzml" lines_diff="4"/> + <extra_files type="file" file="12_combined.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="12_combined.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -493,7 +488,7 @@ <output name="pixel_annotations" file="112_annotation_output.tabular"/> <output name="QC_overview" file="112_auto_combined_QC.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="112_auto_combined.imzml.txt" compare="sim_size"> - <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="4"/> + <extra_files type="file" file="112_auto_combined.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="112_auto_combined.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -507,7 +502,7 @@ <output name="pixel_annotations" file="2123_annotation_output.tabular"/> <output name="QC_overview" file="2123_auto_combined_QC.pdf" compare="sim_size"/> <output name="outfile_imzml" ftype="imzml" file="2123_auto_combined.imzml.txt" compare="sim_size"> - <extra_files type="file" file="2123_auto_combined.imzml" name="imzml" lines_diff="4"/> + <extra_files type="file" file="2123_auto_combined.imzml" name="imzml" lines_diff="12"/> <extra_files type="file" file="2123_auto_combined.ibd" name="ibd" compare="sim_size"/> </output> </test> @@ -558,7 +553,7 @@ **Output** -- MSI data as imzML file (in continous format when m/z axis were the same; in processed format when m/z axis were different) +- MSI data as imzML file (in continuous format when m/z axis were the same; in processed format when m/z axis were different) - Pdf with pixel positions and annotations of the combined files - Tabular file with pixel annotations (x,y,column with input file names and annotation columns)
--- a/macros.xml Fri Dec 13 13:54:23 2019 -0500 +++ b/macros.xml Wed Mar 25 07:02:41 2020 -0400 @@ -1,316 +1,322 @@ -<macros> - <token name="@VERSION@">1.12.1</token> - - <xml name="requirements"> - <requirements> - <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> - <requirement type="package" version="3.5.1">r-base</requirement> - <yield/> - </requirements> - </xml> - - <xml name="print_version"> - <version_command><![CDATA[ -echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ") - ]]></version_command> - </xml> - - <token name="@INPUT_LINKING@"><![CDATA[ - #if $infile.ext == 'imzml' - ln -s '${infile.extra_files_path}/imzml' infile.imzML && - ln -s '${infile.extra_files_path}/ibd' infile.ibd && - #elif $infile.ext == 'analyze75' - ln -s '${infile.extra_files_path}/hdr' infile.hdr && - ln -s '${infile.extra_files_path}/img' infile.img && - ln -s '${infile.extra_files_path}/t2m' infile.t2m && - #else - ln -s $infile infile.RData && - #end if - ]]></token> - - - <token name="@READING_MSIDATA@"><![CDATA[ - ## importing MSI data files - - ## 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', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$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') - #end if - - ]]></token> - - <token name="@DATA_PROPERTIES@"><![CDATA[ - ## Number of features (mz) - maxfeatures = length(features(msidata)) - ## Range mz - minmz = round(min(mz(msidata)), digits=2) - maxmz = round(max(mz(msidata)), digits=2) - ## Number of spectra (pixels) - pixelcount = length(pixels(msidata)) - ## Range x coordinates - minimumx = min(coord(msidata)[,1]) - maximumx = max(coord(msidata)[,1]) - ## Range y coordinates - minimumy = min(coord(msidata)[,2]) - maximumy = max(coord(msidata)[,2]) - - - properties = c("Number of m/z features", - "Range of m/z values", - "Number of pixels", - "Range of x coordinates", - "Range of y coordinates") - - values = c(paste0(maxfeatures), - paste0(minmz, " - ", maxmz), - paste0(pixelcount), - paste0(minimumx, " - ", maximumx), - paste0(minimumy, " - ", maximumy)) - - property_df = data.frame(properties, values) - ]]></token> - - <token name="@READING_MSIDATA_INRAM@"><![CDATA[ - ## importing MSI data files - - ## 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', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") - centroided(msidata) = $centroids - iData(msidata) = iData(msidata)[] - #else - msidata <- readImzML('infile') - centroided(msidata) = $centroids - #end if - #elif $infile.ext == 'analyze75' - msidata = readAnalyze('infile') - centroided(msidata) = $centroids - #else - msidata = loadRData('infile.RData') - #end if - - ]]></token> - - <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ -########################### QC numbers ######################## -## including intensity calculations which need data in RAM - ## Number of features (mz) - maxfeatures = length(features(msidata)) - ## Range mz - minmz = round(min(mz(msidata)), digits=2) - maxmz = round(max(mz(msidata)), digits=2) - ## Number of spectra (pixels) - pixelcount = length(pixels(msidata)) - ## Range x coordinates - minimumx = min(coord(msidata)[,1]) - maximumx = max(coord(msidata)[,1]) - ## Range y coordinates - minimumy = min(coord(msidata)[,2]) - maximumy = max(coord(msidata)[,2]) - ## Range of intensities - minint = round(min(spectra(msidata), na.rm=TRUE), digits=2) - maxint = round(max(spectra(msidata), na.rm=TRUE), digits=2) - ## Number of intensities > 0, for if conditions - npeaks= sum(spectra(msidata)>0, na.rm=TRUE) - ## Number of NA in spectra matrix - NAcount = sum(is.na(spectra(msidata))) - ## Number of NA in spectra matrix - infcount = sum(is.infinite(spectra(msidata))) - ## Number of duplicated coordinates - dupl_coord = sum(duplicated(coord(msidata))) - - properties = c("Number of m/z features", - "Range of m/z values", - "Number of pixels", - "Range of x coordinates", - "Range of y coordinates", - "Range of intensities", - "Number of NA intensities", - "Number of Inf intensities", - "Number of duplicated coordinates") - - values = c(paste0(maxfeatures), - paste0(minmz, " - ", maxmz), - paste0(pixelcount), - paste0(minimumx, " - ", maximumx), - paste0(minimumy, " - ", maximumy), - paste0(minint, " - ", maxint), - paste0(NAcount), - paste0(infcount), - paste0(dupl_coord)) - - property_df = data.frame(properties, values) - ]]></token> - - <token name="@CARDINAL_DESCRIPTION@"><![CDATA[ - Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. - `More information on Cardinal <http://cardinalmsi.org/>`_ - ]]></token> - <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[ - **Input data** - - - MSI 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 <https://ms-imaging.org/wp/imzml/>`_ - - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) - - Cardinal "MSImageSet" data saved as .RData - ]]></token> - <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ - - Optional tabular file with m/z values: - - - One column with numeric m/z values (without empty fields or letters) - - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) - - m/z features outside the m/z range of the input file are ignored - - - :: - - m/z - 100.0 - 100.01 - 100.02 - ... - ... - - ]]></token> - <token name="@MZ_2COLS_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ - - Tabular file with m/z values: - - - One column with numeric m/z values (without empty fields or letters), another column with names for the m/z (m/z column can also be used as name) - - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) - - m/z features outside the m/z range of the input file are ignored - - - :: - - m/z name - 100.0 analyte1 - 100.01 analyte2 - 100.02 analyte3 - ... - ... - - ]]></token> - <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ - - Optional file with pixel coordinates and annotation: - - - Tabular file: One column with x values, one column with y values and one column with annotations - - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) - - Pixel with coordinates outside the coordinates of the input file are ignored - - :: - - x_coord y_coord annotation - 1 1 healthy - 2 1 healthy - 3 1 disease - ... - ... - - ]]></token> - - <xml name="reading_msidata"> - <param name="infile" type="data" format="imzml,rdata,analyze75" - label="MSI data" - help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/> - <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> - <conditional name="processed_cond"> - <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file"> - <option value="no_processed" selected="True">no</option> - <option value="processed">yes</option> - </param> - <when value="no_processed"/> - <when value="processed"> - <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> - <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> - <option value="mz" >mz</option> - <option value="ppm" selected="True" >ppm</option> - </param> - </when> - </conditional> - </xml> - - <xml name="pdf_filename"> - <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name"> - <sanitizer invalid_char=""> - <valid initial="string.ascii_letters,string.digits"> - <add value="_"/> - <add value=" "/> - </valid> - </sanitizer> - </param> - </xml> - - <xml name="sanitizer_multiple_digits"> - <sanitizer invalid_char=""> - <valid initial="string.digits"> - <add value=":" /> - <add value="," /> - </valid> - </sanitizer> - </xml> - - <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features"> - <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/> - <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/> - <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> - </xml> - - <xml name="reading_2_column_mz_tabular" token_optional="false"> - <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular" - label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/> - <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/> - <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/> - <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> - </xml> - - <xml name="reading_pixel_annotations"> - <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation" - help="Tabular file with three columns: x values, y values and pixel annotations"/> - <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/> - <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/> - <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/> - <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> - </xml> - - <xml name="citations"> - <citations> - <citation type="doi">10.1093/bioinformatics/btv146</citation> - </citations> - </xml> - <xml name="infile_analyze75"> - <param name="infile" value="" ftype="analyze75"> - <composite_data value="Analyze75.hdr"/> - <composite_data value="Analyze75.img"/> - <composite_data value="Analyze75.t2m"/> - </param> - </xml> - <xml name="infile_imzml"> - <param name="infile" value="" ftype="imzml"> - <composite_data value="Example_Continuous.imzML"/> - <composite_data value="Example_Continuous.ibd"/> - </param> - </xml> -</macros> +<macros> + <token name="@VERSION@">1.12.1</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> + <requirement type="package" version="3.5.1">r-base</requirement> + <yield/> + </requirements> + </xml> + + <xml name="print_version"> + <version_command><![CDATA[ +echo $(R --version | grep version | grep -v GNU)", Cardinal version" $(R --vanilla --slave -e "library(Cardinal); cat(sessionInfo()\$otherPkgs\$Cardinal\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + </xml> + + <token name="@INPUT_LINKING@"><![CDATA[ + #if $infile.ext == 'imzml' + ln -s '${infile.extra_files_path}/imzml' infile.imzML && + ln -s '${infile.extra_files_path}/ibd' infile.ibd && + #elif $infile.ext == 'analyze75' + ln -s '${infile.extra_files_path}/hdr' infile.hdr && + ln -s '${infile.extra_files_path}/img' infile.img && + ln -s '${infile.extra_files_path}/t2m' infile.t2m && + #else + ln -s $infile infile.RData && + #end if + ]]></token> + + + <token name="@READING_MSIDATA@"><![CDATA[ + ## importing MSI data files + + ## 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', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$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') + #end if + + ]]></token> + + <token name="@DATA_PROPERTIES@"><![CDATA[ + ## Number of features (mz) + maxfeatures = length(features(msidata)) + ## Range mz + minmz = round(min(mz(msidata)), digits=2) + maxmz = round(max(mz(msidata)), digits=2) + ## Number of spectra (pixels) + pixelcount = length(pixels(msidata)) + ## Range x coordinates + minimumx = min(coord(msidata)[,1]) + maximumx = max(coord(msidata)[,1]) + ## Range y coordinates + minimumy = min(coord(msidata)[,2]) + maximumy = max(coord(msidata)[,2]) + + + properties = c("Number of m/z features", + "Range of m/z values", + "Number of pixels", + "Range of x coordinates", + "Range of y coordinates") + + values = c(paste0(maxfeatures), + paste0(minmz, " - ", maxmz), + paste0(pixelcount), + paste0(minimumx, " - ", maximumx), + paste0(minimumy, " - ", maximumy)) + + property_df = data.frame(properties, values) + ]]></token> + + <token name="@READING_MSIDATA_INRAM@"><![CDATA[ + ## importing MSI data files + + ## 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', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units") + centroided(msidata) = $centroids + iData(msidata) = iData(msidata)[] + #else + msidata <- readImzML('infile') + centroided(msidata) = $centroids + #end if + #elif $infile.ext == 'analyze75' + msidata = readAnalyze('infile') + centroided(msidata) = $centroids + #else + msidata = loadRData('infile.RData') + #end if + + ]]></token> + + <token name="@DATA_PROPERTIES_INRAM@"><![CDATA[ +########################### QC numbers ######################## +## including intensity calculations which need data in RAM + ## Number of features (mz) + maxfeatures = length(features(msidata)) + ## Range mz + minmz = round(min(mz(msidata)), digits=2) + maxmz = round(max(mz(msidata)), digits=2) + ## Number of spectra (pixels) + pixelcount = length(pixels(msidata)) + ## Range x coordinates + minimumx = min(coord(msidata)[,1]) + maximumx = max(coord(msidata)[,1]) + ## Range y coordinates + minimumy = min(coord(msidata)[,2]) + maximumy = max(coord(msidata)[,2]) + ## Range of intensities + minint = round(min(spectra(msidata), na.rm=TRUE), digits=2) + maxint = round(max(spectra(msidata), na.rm=TRUE), digits=2) + ## Number of intensities > 0, for if conditions + npeaks= sum(spectra(msidata)>0, na.rm=TRUE) + ## Number of NA in spectra matrix + NAcount = sum(is.na(spectra(msidata))) + ## Number of NA in spectra matrix + infcount = sum(is.infinite(spectra(msidata))) + ## Number of duplicated coordinates + dupl_coord = sum(duplicated(coord(msidata))) + + properties = c("Number of m/z features", + "Range of m/z values", + "Number of pixels", + "Range of x coordinates", + "Range of y coordinates", + "Range of intensities", + "Number of NA intensities", + "Number of Inf intensities", + "Number of duplicated coordinates") + + values = c(paste0(maxfeatures), + paste0(minmz, " - ", maxmz), + paste0(pixelcount), + paste0(minimumx, " - ", maximumx), + paste0(minimumy, " - ", maximumy), + paste0(minint, " - ", maxint), + paste0(NAcount), + paste0(infcount), + paste0(dupl_coord)) + + property_df = data.frame(properties, values) + ]]></token> + + <token name="@CARDINAL_DESCRIPTION@"><![CDATA[ + Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. + `More information on Cardinal <http://cardinalmsi.org/>`_ + ]]></token> + <token name="@MSIDATA_INPUT_DESCRIPTION@"><![CDATA[ + **Input data** + + - MSI 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 <https://ms-imaging.org/wp/imzml/>`_ + - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) + - Cardinal "MSImageSet" data saved as .RData + ]]></token> + <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ + - Optional tabular file with m/z values: + + - One column with numeric m/z values (without empty fields or letters) + - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) + - m/z features outside the m/z range of the input file are ignored + + + :: + + m/z + 100.0 + 100.01 + 100.02 + ... + ... + + ]]></token> + <token name="@MZ_2COLS_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ + - Tabular file with m/z values: + + - One column with numeric m/z values (without empty fields or letters), another column with names for the m/z (m/z column can also be used as name) + - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) + - m/z features outside the m/z range of the input file are ignored + + + :: + + m/z name + 100.0 analyte1 + 100.01 analyte2 + 100.02 analyte3 + ... + ... + + ]]></token> + <token name="@SPECTRA_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ + - Optional file with pixel coordinates and annotation: + + - Tabular file: One column with x values, one column with y values and one column with annotations + - The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes) + - Pixel with coordinates outside the coordinates of the input file are ignored + + :: + + x_coord y_coord annotation + 1 1 healthy + 2 1 healthy + 3 1 disease + ... + ... + + ]]></token> + + <xml name="reading_msidata"> + <param name="infile" type="data" format="imzml,rdata,analyze75" + label="MSI data" + help="Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)"/> + <param name="centroids" type="boolean" label="Centroided input" help="Choose Yes if peak detection has already been done." truevalue="TRUE" falsevalue="FALSE"/> + <conditional name="processed_cond"> + <param name="processed_file" type="select" label="Processed imzML file" help="Choose no if your input is an Analyze7.5 or continuous imzML file"> + <option value="no_processed" selected="True">no</option> + <option value="processed">yes</option> + </param> + <when value="no_processed"/> + <when value="processed"> + <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> + <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> + <option value="mz" >mz</option> + <option value="ppm" selected="True" >ppm</option> + </param> + </when> + </conditional> + </xml> + + <xml name="pdf_filename"> + <param name="filename" type="text" value="" label="Title" help="Will appear in the pdf output, if nothing given it will take the dataset name"> + <sanitizer invalid_char=""> + <valid initial="string.ascii_letters,string.digits"> + <add value="_"/> + <add value=" "/> + </valid> + </sanitizer> + </param> + </xml> + + <xml name="sanitizer_multiple_digits"> + <sanitizer invalid_char=""> + <valid initial="string.digits"> + <add value=":" /> + <add value="," /> + </valid> + </sanitizer> + </xml> + + <xml name="reading_1_column_mz_tabular" token_label="Tabular file with m/z features"> + <param name="mz_tabular" type="data" format="tabular" label="@LABEL@" help="Only numeric m/z values are allowed"/> + <param name="feature_column" data_ref="mz_tabular" label="Column with features" type="data_column"/> + <param name="feature_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> + </xml> + + <xml name="reading_2_column_mz_tabular" token_optional="false"> + <param name="calibrant_file" type="data" optional="@OPTIONAL@" format="tabular" + label="m/z of interest (e.g. internal Calibrants)" help="one column with m/z values, optional second column with names (m/z values can also be selected as name)"/> + <param name="mz_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with m/z values" type="data_column"/> + <param name="name_column" data_ref="calibrant_file" optional="@OPTIONAL@" label="Column with name of m/z values" type="data_column"/> + <param name="calibrant_header" type="boolean" optional="@OPTIONAL@" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> + </xml> + + <xml name="reading_pixel_annotations"> + <param name="annotation_file" type="data" format="tabular" label="Tabular file with pixel coordinates and annotation" + help="Tabular file with three columns: x values, y values and pixel annotations"/> + <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/> + <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/> + <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/> + <param name="tabular_header" type="boolean" label="Tabular file contains a header line" truevalue="TRUE" falsevalue="FALSE"/> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btv146</citation> + </citations> + </xml> + <xml name="infile_analyze75"> + <param name="infile" value="" ftype="analyze75"> + <composite_data value="Analyze75.hdr"/> + <composite_data value="Analyze75.img"/> + <composite_data value="Analyze75.t2m"/> + </param> + </xml> + <xml name="infile_imzml"> + <param name="infile" value="" ftype="imzml"> + <composite_data value="Example_Continuous.imzML"/> + <composite_data value="Example_Continuous.ibd"/> + </param> + </xml> + <xml name="processed_infile_imzml"> + <param name="infile" value="" ftype="imzml"> + <composite_data value="Example_Processed.imzML"/> + <composite_data value="Example_Processed.ibd"/> + </param> + </xml> +</macros>
--- a/test-data/out3.imzml Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/out3.imzml Wed Mar 25 07:02:41 2020 -0400 @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{AEDF2DEE-A321-4DAF-B971-943AE2AF79A6}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="8311A159EC925605745E409F14BB6C570FF59ACA" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="7cde7a72-9a6b-4ed9-a809-79ca20bf45b4" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4a26497a6ddfc9a61e9c0e463e4c246c5d734f80" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -22,19 +22,18 @@ </referenceableParamGroup> <referenceableParamGroup id="scan1"> <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" /> - <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" /> </referenceableParamGroup> <referenceableParamGroup id="mzArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> <referenceableParamGroup id="intensityArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> @@ -43,18 +42,24 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="1.12.1"> + <software id="Cardinal" version="2.4.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> <scanSettingsList count="1"> <scanSettings id="scansettings1"> <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" /> - <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="2" /> + <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="1" /> + <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="2" /> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" /> + <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="Inf" /> </scanSettings> </scanSettingsList> <instrumentConfigurationList count="1"> - <instrumentConfiguration id="IC1" /> + <instrumentConfiguration id="IC1"> + <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" /> + </instrumentConfiguration> </instrumentConfigurationList> <dataProcessingList count="1"> <dataProcessing id="CardinalWriteImzML"> @@ -73,6 +78,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -100,6 +107,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -127,6 +136,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2">
--- a/test-data/out3.imzml.txt Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/out3.imzml.txt Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 9616 Feb 12 19:18 ibd --rw-r--r-- 1 meli meli 8282 Feb 12 19:18 imzml +-rw-r--r-- 1 meli meli 9616 Mär 24 20:25 ibd +-rw-r--r-- 1 meli meli 8958 Mär 24 20:25 imzml
--- a/test-data/out4.imzml Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/out4.imzml Wed Mar 25 07:02:41 2020 -0400 @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{2567A8C4-D2AF-4C81-874C-82E9134A080C}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="EA722C9CF5A229ACF6AEAD177908D73A1C8CB44E" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="b0dec95e-b66f-4c3f-86df-166d942f42c3" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d9b557cf2c0e15a0cdd863e50897b07a55a26f31" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -22,19 +22,18 @@ </referenceableParamGroup> <referenceableParamGroup id="scan1"> <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" /> - <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" /> </referenceableParamGroup> <referenceableParamGroup id="mzArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> <referenceableParamGroup id="intensityArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> @@ -43,18 +42,24 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="1.12.1"> + <software id="Cardinal" version="2.4.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> <scanSettingsList count="1"> <scanSettings id="scansettings1"> - <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="2.000000" /> + <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" /> </scanSettings> </scanSettingsList> <instrumentConfigurationList count="1"> - <instrumentConfiguration id="IC1" /> + <instrumentConfiguration id="IC1"> + <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" /> + </instrumentConfiguration> </instrumentConfigurationList> <dataProcessingList count="1"> <dataProcessing id="CardinalWriteImzML"> @@ -73,6 +78,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -100,6 +107,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="1" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="1.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -127,6 +136,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -154,6 +165,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -181,6 +194,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2">
--- a/test-data/out4.imzml.txt Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/out4.imzml.txt Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ imzML file: total 44 --rw-r--r-- 1 meli meli 28792 Feb 12 00:49 ibd --rw-r--r-- 1 meli meli 11141 Feb 12 00:49 imzml +-rw-r--r-- 1 meli meli 28792 Mär 24 19:23 ibd +-rw-r--r-- 1 meli meli 12046 Mär 24 19:23 imzml
--- a/test-data/out5.imzml Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/out5.imzml Wed Mar 25 07:02:41 2020 -0400 @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{CC0B2B92-FB40-42C8-822F-834AA528954C}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0B644915E88274BE83FBB110D4CC6D0CDFABAAAC" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="87b0ab73-abe6-4eb6-91ba-b6d493a343bc" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9de3a02d0943ecda0717845511a8f7b8f58d1db7" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -22,19 +22,18 @@ </referenceableParamGroup> <referenceableParamGroup id="scan1"> <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" /> - <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" /> </referenceableParamGroup> <referenceableParamGroup id="mzArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> <referenceableParamGroup id="intensityArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> @@ -43,18 +42,24 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="1.12.1"> + <software id="Cardinal" version="2.4.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> <scanSettingsList count="1"> <scanSettings id="scansettings1"> <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="3" /> - <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="2" /> + <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" /> + <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" /> </scanSettings> </scanSettingsList> <instrumentConfigurationList count="1"> - <instrumentConfiguration id="IC1" /> + <instrumentConfiguration id="IC1"> + <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" /> + </instrumentConfiguration> </instrumentConfigurationList> <dataProcessingList count="1"> <dataProcessing id="CardinalWriteImzML"> @@ -73,6 +78,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -100,6 +107,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -127,6 +136,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="2" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="2.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -154,6 +165,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="1" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="1.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -181,6 +194,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="2" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="2.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2"> @@ -208,6 +223,8 @@ <referenceableParamGroupRef ref="scan1" /> <cvParam cvRef="IMS" accession="IMS:1000050" name="position x" value="3" /> <cvParam cvRef="IMS" accession="IMS:1000051" name="position y" value="3" /> + <userParam name="3DPositionX" value="3.000000" /> + <userParam name="3DPositionY" value="3.000000" /> </scan> </scanList> <binaryDataArrayList count="2">
--- a/test-data/out5.imzml.txt Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/out5.imzml.txt Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ imzML file: total 20 --rw-r--r-- 1 meli meli 380 Feb 12 00:50 ibd --rw-r--r-- 1 meli meli 12508 Feb 12 00:50 imzml +-rw-r--r-- 1 meli meli 380 Mär 24 19:24 ibd +-rw-r--r-- 1 meli meli 13525 Mär 24 19:24 imzml
--- a/test-data/out6.imzml Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/out6.imzml Wed Mar 25 07:02:41 2020 -0400 @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{24BF18EC-E1DE-4B67-BC12-C3EB475CFC0A}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="DA0417F6AA4EDD71F808B6EA0D7A0706737464EB" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="8b625a26-987e-4e32-b7d4-729efe840814" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="78e6eb56507d789575ee0495e60f9d44a192c0dd" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -22,19 +22,18 @@ </referenceableParamGroup> <referenceableParamGroup id="scan1"> <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" /> - <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" /> </referenceableParamGroup> <referenceableParamGroup id="mzArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> <referenceableParamGroup id="intensityArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> @@ -43,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - 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--- a/test-data/out6.imzml.txt Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/out6.imzml.txt Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ imzML file: total 164 --rw-r--r-- 1 meli meli 146896 Feb 12 00:51 ibd --rw-r--r-- 1 meli meli 16868 Feb 12 00:51 imzml +-rw-r--r-- 1 meli meli 146896 Mär 24 19:25 ibd +-rw-r--r-- 1 meli meli 18221 Mär 24 19:25 imzml
--- a/test-data/out7.imzml Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/out7.imzml Wed Mar 25 07:02:41 2020 -0400 @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{B095BB77-684D-4BFF-82D3-B76D0EB1C0CD}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="628A551B81DCF301B65E3A5AB1182F0BF319533C" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="bf61653e-aa1a-4f9a-a84d-3ff3435ee7fe" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="352c33defde6728b7dfb83e18ed1c433fa4b8697" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -22,19 +22,18 @@ </referenceableParamGroup> <referenceableParamGroup id="scan1"> <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" /> - 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--- a/test-data/out7.imzml.txt Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/out7.imzml.txt Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ imzML file: total 116 --rw-r--r-- 1 meli meli 95976 Feb 12 00:51 ibd --rw-r--r-- 1 meli meli 16846 Feb 12 00:51 imzml +-rw-r--r-- 1 meli meli 95976 Mär 24 19:26 ibd +-rw-r--r-- 1 meli meli 18199 Mär 24 19:26 imzml
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out8.imzml.txt Wed Mar 25 07:02:41 2020 -0400 @@ -0,0 +1,4 @@ +imzML file: +total 348 +-rw-r--r-- 1 meli meli 335976 Mär 24 19:27 ibd +-rw-r--r-- 1 meli meli 12402 Mär 24 19:27 imzml
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--- a/test-data/preprocessing_results1.imzml.txt Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/preprocessing_results1.imzml.txt Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 96 Feb 24 14:11 ibd --rw-r--r-- 1 meli meli 16714 Feb 24 14:11 imzml +-rw-r--r-- 1 meli meli 216 Mär 24 10:39 ibd +-rw-r--r-- 1 meli meli 18090 Mär 24 10:39 imzml
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--- a/test-data/preprocessing_results2.imzml.txt Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/preprocessing_results2.imzml.txt Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ imzML file: -total 80 --rw-r--r-- 1 meli meli 54720 Feb 24 14:12 ibd --rw-r--r-- 1 meli meli 21132 Feb 24 14:12 imzml +total 64 +-rw-r--r-- 1 meli meli 37404 Mär 24 10:40 ibd +-rw-r--r-- 1 meli meli 22796 Mär 24 10:40 imzml
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--- a/test-data/preprocessing_results3.imzml.txt Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/preprocessing_results3.imzml.txt Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ imzML file: -total 36 --rw-r--r-- 1 meli meli 14216 Feb 24 14:12 ibd --rw-r--r-- 1 meli meli 16824 Feb 24 14:12 imzml +total 24 +-rw-r--r-- 1 meli meli 136 Mär 24 11:10 ibd +-rw-r--r-- 1 meli meli 18088 Mär 24 11:10 imzml
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--- a/test-data/preprocessing_results4.imzml.txt Fri Dec 13 13:54:23 2019 -0500 +++ b/test-data/preprocessing_results4.imzml.txt Wed Mar 25 07:02:41 2020 -0400 @@ -1,4 +1,4 @@ imzML file: -total 28 --rw-r--r-- 1 meli meli 6376 Feb 24 14:13 ibd --rw-r--r-- 1 meli meli 16801 Feb 24 14:13 imzml +total 84 +-rw-r--r-- 1 meli meli 63256 Mär 24 11:35 ibd +-rw-r--r-- 1 meli meli 18199 Mär 24 11:35 imzml
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