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Update Cardinal Version 3.4.3 #763
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aa7f3c5
change description
MarenStillger b44dfc6
change description
MarenStillger f841786
Initial commit
MarenStillger 4c10440
Change description
MarenStillger 4fb6609
Fix tests
MarenStillger efeb016
Fix test
MarenStillger db40ec0
Fix version token in requirements
MarenStillger 308bd65
Fix tests and requirements
MarenStillger e3e7d8d
Fix tests
MarenStillger a1f3bd7
Fix tests
MarenStillger 16c814a
Merge branch 'master' into Update_test
bgruening 6732b02
Fix input linking
MarenStillger 4f54d86
Merge remote-tracking branch 'origin/Update_test' into Update_test
MarenStillger a402082
Fix tests
MarenStillger 6e1eb51
Fix tests
MarenStillger 8bef62c
Fix tests
MarenStillger 371f840
Fix profile and requirements
MarenStillger 523c7c8
Merge branch 'master' into Update_test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,9 @@ | ||
| <tool id="cardinal_colocalization" name="MSI colocalization" version="@[email protected]"> | ||
| <tool id="cardinal_colocalization" name="MSI colocalization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> | ||
| <description>mass spectrometry imaging colocalization</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"> | ||
| <requirement type="package" version="2.3">r-gridextra</requirement> | ||
| </expand> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"> | ||
| <![CDATA[ | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,25 +1,21 @@ | ||
| <tool id="cardinal_combine" name="MSI combine" version="@[email protected]"> | ||
| <tool id="cardinal_combine" name="MSI combine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> | ||
| <description> | ||
| combine several mass spectrometry imaging datasets into one | ||
| </description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"> | ||
| <requirement type="package" version="3.3.5">r-ggplot2</requirement> | ||
| <requirement type="package" version="0.12">r-maldiquantforeign</requirement> | ||
| <requirement type="package" version="1.20">r-maldiquant</requirement> | ||
| </expand> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="exit_code"> | ||
| <![CDATA[ | ||
| #for $i, $infile in enumerate($infiles): | ||
| #if $infile.ext == 'imzml' | ||
| ln -s '${infile.extra_files_path}/imzml' infile_${i}.imzML && | ||
| ln -s '${infile.extra_files_path}/ibd' infile_${i}.ibd && | ||
| cp '${infile.extra_files_path}/imzml' infile_${i}.imzML && | ||
| cp '${infile.extra_files_path}/ibd' infile_${i}.ibd && | ||
| #elif $infile.ext == 'analyze75' | ||
| ln -s '${infile.extra_files_path}/hdr' infile_${i}.hdr && | ||
| ln -s '${infile.extra_files_path}/img' infile_${i}.img && | ||
| ln -s '${infile.extra_files_path}/t2m' infile_${i}.t2m && | ||
| cp '${infile.extra_files_path}/hdr' infile_${i}.hdr && | ||
| cp '${infile.extra_files_path}/img' infile_${i}.img && | ||
| cp '${infile.extra_files_path}/t2m' infile_${i}.t2m && | ||
| #else | ||
| ln -s '$infile' infile_${i}.RData && | ||
| #end if | ||
|
|
@@ -103,14 +99,8 @@ all_files = $num_infiles | |
| get(ls()[ls() != "fileName"]) | ||
| } | ||
| msidata_$i = loadRData('infile_${i}.RData') | ||
| ## keep compatibility with old .RData files: | ||
| msidata_$i\$column1 = NULL | ||
| msidata_$i\$column2 = NULL | ||
| msidata_$i\$column3 = NULL | ||
| msidata_$i\$column4 = NULL | ||
| msidata_$i\$column5 = NULL | ||
| msidata_$i\$combined_sample = NULL | ||
| msidata_$i <- as(msidata_$i, "MSImagingExperiment") | ||
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| #end if | ||
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| ## remove duplicated coordinates, otherwise combine will fail | ||
|
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@@ -128,7 +118,6 @@ all_files = $num_infiles | |
| ############ 3) Read and process annotation tabular files ###################### | ||
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| #if str($annotation_cond.annotation_tabular) == 'annotation' | ||
| print("annotations") | ||
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| ## read annotation tabular, set first two columns as x and y, merge with coordinates dataframe and order according to pixelorder in msidata | ||
| input_annotation = read.delim("annotation_file_${i}.tabular", header = $annotation_cond.tabular_header, stringsAsFactors = FALSE) | ||
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@@ -138,7 +127,7 @@ all_files = $num_infiles | |
| colnames(msidata_coordinates)[3] = "pixel_index" | ||
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| annotation_df = merge(msidata_coordinates, input_annotation, by=c("x", "y"), all.x=TRUE) | ||
| annotation_df_sorted = annotation_df[order(annotation_df\$pixel_index),]## orders pixel according to msidata | ||
| annotation_df_sorted = annotation_df[order(annotation_df\$pixel_index),] | ||
| annotation_df_sorted\$pixel_index = NULL | ||
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| ## extract columnnames from (last) annotation tabular (for QC plot names) | ||
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@@ -171,7 +160,7 @@ all_files = $num_infiles | |
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| #elif str( $combine_conditional.combine_method ) == 'automatic_combine': | ||
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| ## use name of Galaxy inputfile as sample annotation | ||
| ## use name of Galaxy input file as sample annotation | ||
| sample_name = character() | ||
| #set escaped_element_identifier = re.sub('[^\w\-\s\[/]]', '_', str($infile.element_identifier)) | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| <tool id="cardinal_data_exporter" name="MSI data exporter" version="@[email protected]"> | ||
| <tool id="cardinal_data_exporter" name="MSI data exporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> | ||
| <description> | ||
| exports imzML and Analyze7.5 to tabular files | ||
| </description> | ||
|
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@@ -102,7 +102,7 @@ if (class(msidata) == "MSImageSet"){ | |
| count = 1 | ||
| for (subsample in levels(msidata\$annotation)){ | ||
| subsample_pixels = msidata[,msidata\$annotation == subsample] | ||
| subsample_calc = rowMeans(spectra(subsample_pixels), na.rm=TRUE) | ||
| subsample_calc = rowMeans(as.matrix(spectra(subsample_pixels)), na.rm=TRUE) | ||
| sample_matrix = cbind(sample_matrix, subsample_calc) | ||
| count = count+1} | ||
| sample_matrix_mean = cbind(mz_names,sample_matrix) | ||
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@@ -117,7 +117,7 @@ if (class(msidata) == "MSImageSet"){ | |
| count = 1 | ||
| for (subsample in levels(msidata\$annotation)){ | ||
| subsample_pixels = msidata[,msidata\$annotation == subsample] | ||
| subsample_calc = apply(spectra(subsample_pixels),1,median, na.rm=TRUE) | ||
| subsample_calc = apply(as.matrix(spectra(subsample_pixels)),1,median, na.rm=TRUE) | ||
| sample_matrix = cbind(sample_matrix, subsample_calc) | ||
| count = count+1} | ||
| sample_matrix_median = cbind(mz_names,sample_matrix) | ||
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@@ -190,13 +190,13 @@ if (class(msidata) == "MSImageSet"){ | |
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| for (mass in 1:length(inputcalibrantmasses)){ | ||
| filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],] | ||
| if (nrow(filtered_data) > 1 & sum(spectra(filtered_data),na.rm=TRUE) > 0){ | ||
| if (nrow(filtered_data) > 1 & sum(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0){ | ||
| ## intensity of all m/z > 0 | ||
| intensity_sum = colSums(spectra(filtered_data), na.rm=TRUE) > 0 | ||
| intensity_sum = colSums(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0 | ||
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| }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data), na.rm=TRUE) > 0){ | ||
| }else if(nrow(filtered_data) == 1 & sum(as.matrix(spectra(filtered_data)), na.rm=TRUE) > 0){ | ||
| ## intensity of only m/z > 0 | ||
| intensity_sum = spectra(filtered_data) > 0 | ||
| intensity_sum = as.matrix(spectra(filtered_data)) > 0 | ||
| }else{ | ||
| intensity_sum = rep(FALSE, ncol(filtered_data))} | ||
| ## for each pixel add sum of intensities > 0 in the given m/z range | ||
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@@ -343,7 +343,11 @@ if (class(msidata) == "MSImageSet"){ | |
| <param name="feature_header" value="False"/> | ||
| <param name="plusminus_ppm" value="200"/> | ||
| </conditional> | ||
| <output name="feature_output" file="features_out4.tabular"/> | ||
| <output name="feature_output"> | ||
| <assert_contents> | ||
| <has_text text="100.120072029209"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="pixel_output" file="pixel_out4.tabular"/> | ||
| </test> | ||
| </tests> | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,9 @@ | ||
| <tool id="cardinal_filtering" name="MSI filtering" version="@[email protected]"> | ||
| <tool id="cardinal_filtering" name="MSI filtering" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> | ||
| <description>tool for filtering mass spectrometry imaging data</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"> | ||
| <requirement type="package" version="2.3">r-gridextra</requirement> | ||
| <requirement type="package" version="3.3.5">r-ggplot2</requirement> | ||
| </expand> | ||
| <expand macro="requirements"/> | ||
| <expand macro="print_version"/> | ||
| <command detect_errors="exit_code"> | ||
| <![CDATA[ | ||
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,13 +1,11 @@ | ||
| <tool id="cardinal_mz_images" name="MSI mz images" version="@[email protected]"> | ||
| <tool id="cardinal_mz_images" name="MSI mz images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> | ||
| <description> | ||
| mass spectrometry imaging m/z heatmaps | ||
| </description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"> | ||
| <requirement type="package" version="2.3">r-gridextra</requirement> | ||
| </expand> | ||
| <expand macro="requirements"/> | ||
| <command detect_errors="aggressive"> | ||
| <![CDATA[ | ||
| @INPUT_LINKING@ | ||
|
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@@ -83,8 +81,8 @@ if (ncol(msidata)>0 & nrow(msidata) >0){ | |
| print("svg pixel image") | ||
| ## reverse y axis for svg output = correct order and nice svg image | ||
| coord(msidata)\$y <- max(coord(msidata)\$y) - coord(msidata)\$y + 1 | ||
| ## works only with MSImageSet as expected | ||
| msidata = as(msidata, "MSImageSet") | ||
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| msidata = as(msidata,"MSImagingExperiment") | ||
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| svg(file="svg_pixel_output.svg", width=maximumx, height=maximumy) | ||
| par(mar=c(0,0,0,0), oma=c(0,0,0,0))## no margin for svg | ||
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@@ -132,7 +130,7 @@ dev.off() | |
| <expand macro="pdf_filename"/> | ||
| <expand macro="reading_2_column_mz_tabular"/> | ||
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| <param name="plusminus_dalton" value="0.25" type="float" label="plusminus m/" help="m/z range to add on either side of the given m/z to create a window in which the mean of all intensities will be computed"/> | ||
| <param name="plusminus_dalton" value="0.25" type="float" label="plusminus m/z" help="m/z range to add on either side of the given m/z to create a window in which the mean of all intensities will be computed"/> | ||
| <param name="image_contrast" type="select" label="Contrast enhancement" help="The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots"> | ||
| <option value="none" selected="True">none</option> | ||
| <option value="suppression">suppression</option> | ||
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@@ -193,7 +191,7 @@ dev.off() | |
| </data> | ||
| </outputs> | ||
| <tests> | ||
| <test> | ||
| <test expect_num_outputs="1"> | ||
| <expand macro="infile_imzml"/> | ||
| <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> | ||
| <param name="mz_column" value="1"/> | ||
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@@ -204,7 +202,7 @@ dev.off() | |
| <param name="colorkey" value="True"/> | ||
| <output name="plots" file="Heatmaps_imzml.pdf" ftype="pdf" compare="sim_size"/> | ||
| </test> | ||
| <test> | ||
| <test expect_num_outputs="2"> | ||
| <expand macro="infile_analyze75"/> | ||
| <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/> | ||
| <param name="mz_column" value="1"/> | ||
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@@ -218,7 +216,7 @@ dev.off() | |
| <output name="plots" file="Heatmaps_analyze75.pdf" ftype="pdf" compare="sim_size"/> | ||
| <output name="svg_output" file="analyze75.svg" ftype="svg" compare="sim_size"/> | ||
| </test> | ||
| <test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="infile" value="preprocessed.RData" ftype="rdata"/> | ||
| <param name="calibrant_file" value="inputpeptides.tabular" ftype="tabular"/> | ||
| <param name="mz_column" value="1"/> | ||
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@@ -228,7 +226,7 @@ dev.off() | |
| <param name="filename" value="Testfile_rdata"/> | ||
| <output name="plots" file="Heatmaps_rdata.pdf" ftype="pdf" compare="sim_size"/> | ||
| </test> | ||
| <test> | ||
| <test expect_num_outputs="1"> | ||
| <param name="infile" value="empty_spectra.rdata" ftype="rdata"/> | ||
| <param name="calibrant_file" value="inputpeptides2.tabular" ftype="tabular"/> | ||
| <param name="mz_column" value="1"/> | ||
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@@ -239,7 +237,7 @@ dev.off() | |
| <param name="filename" value="Testfile_rdata"/> | ||
| <output name="plots" file="Heatmaps_LM8_file16.pdf" ftype="pdf" compare="sim_size"/> | ||
| </test> | ||
| <test> | ||
| <test expect_num_outputs="1"> | ||
| <expand macro="processed_infile_imzml"/> | ||
| <conditional name="processed_cond"> | ||
| <param name="processed_file" value="processed"/> | ||
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Is copying really necessary?
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unfortunately yes, otherwise neither imzml nor analyze75 files will be loaded