Mercurial > repos > galaxyp > cardinal_preprocessing
diff macros.xml @ 6:5bf056c0354e draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 15e24b1f0143679647906bc427654f66b417a45c"
| author | galaxyp |
|---|---|
| date | Wed, 25 Mar 2020 08:13:17 -0400 |
| parents | 141a9288be9c |
| children | 44a4b31fcbf3 |
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--- a/macros.xml Fri Dec 13 13:57:13 2019 -0500 +++ b/macros.xml Wed Mar 25 08:13:17 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>