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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0 |
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modified:
msi_filtering.xml test-data/Analyze75.hdr test-data/Analyze75.img test-data/Analyze75.t2m test-data/analyze75_filtered2.pdf test-data/analyze_filtered.RData test-data/analyze_filtered.pdf test-data/analyze_matrix.tabular test-data/analyze_originaloutput2.RData test-data/featuresofinterest2.tabular test-data/imzml_filtered.RData test-data/imzml_filtered.pdf test-data/imzml_filtered2.RData test-data/imzml_filtered2.pdf test-data/imzml_filtered3.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.RData test-data/imzml_filtered4.pdf test-data/imzml_filtered5.RData test-data/imzml_filtered5.pdf test-data/imzml_matrix3.tabular test-data/inputpixels2.tabular test-data/inputpixels_2column.tabular test-data/rdata_matrix.tabular test-data/rdata_notfiltered.RData |
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added:
test-data/analyze_filteredoutside.RData test-data/inputpixels_2column_challenge.tabular test-data/preprocessed.RData |
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removed:
test-data/preprocessing_results1.RData |
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| diff -r 98c101b19f3c -r 22db5eb94e50 msi_filtering.xml --- a/msi_filtering.xml Mon Apr 23 17:18:35 2018 -0400 +++ b/msi_filtering.xml Mon May 28 12:36:24 2018 -0400 |
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| b'@@ -1,19 +1,19 @@\n-<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.7.0.1">\n+<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.0">\n <description>tool for filtering mass spectrometry imaging data</description>\n <requirements>\n- <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>\n+ <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>\n <requirement type="package" version="2.2.1">r-gridextra</requirement>\n </requirements>\n <command detect_errors="exit_code">\n <![CDATA[\n \n #if $infile.ext == \'imzml\'\n- cp \'${infile.extra_files_path}/imzml\' infile.imzML &&\n- cp \'${infile.extra_files_path}/ibd\' infile.ibd &&\n+ ln -s \'${infile.extra_files_path}/imzml\' infile.imzML &&\n+ ln -s \'${infile.extra_files_path}/ibd\' infile.ibd &&\n #elif $infile.ext == \'analyze75\'\n- cp \'${infile.extra_files_path}/hdr\' infile.hdr &&\n- cp \'${infile.extra_files_path}/img\' infile.img &&\n- cp \'${infile.extra_files_path}/t2m\' infile.t2m &&\n+ ln -s \'${infile.extra_files_path}/hdr\' infile.hdr &&\n+ ln -s \'${infile.extra_files_path}/img\' infile.img &&\n+ ln -s \'${infile.extra_files_path}/t2m\' infile.t2m &&\n #else\n ln -s $infile infile.RData &&\n #end if\n@@ -27,23 +27,21 @@\n <configfile name="MSI_subsetting"><![CDATA[\n \n \n-################################# load libraries and read file #########################\n+################################# load libraries and read file #################\n \n \n library(Cardinal)\n library(gridExtra)\n \n-## Read MALDI Imaging dataset\n-\n #if $infile.ext == \'imzml\'\n- msidata = readMSIData(\'infile.imzML\')\n+ msidata = readImzML(\'infile\')\n #elif $infile.ext == \'analyze75\'\n- msidata = readMSIData(\'infile.hdr\')\n+ msidata = readAnalyze(\'infile\')\n #else\n load(\'infile.RData\')\n #end if\n \n-###################################### inputfile properties in numbers ######################\n+##################################### QC: inputfile properties in numbers ######\n \n #if $outputs.outputs_select == "quality_control":\n ## Number of features (mz)\n@@ -75,12 +73,13 @@\n #end if\n \n \n-###################################### filtering of pixels ######################\n+###################################### Filtering of pixels #####################\n+\n+### Pixels in the one column format "x=,y="\n \n #if str($pixels_cond.pixel_filtering) == "single_column":\n print("single column")\n \n- #if $pixels_cond.single_pixels:\n input_list = read.delim("$pixels_cond.single_pixels", header = FALSE, stringsAsFactors = FALSE)\n numberpixels = length(input_list[,$pixels_cond.pixel_column])\n valid_entries = input_list[,$pixels_cond.pixel_column] %in% names(pixels(msidata))\n@@ -91,19 +90,16 @@\n pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[valid_entries,$pixels_cond.pixel_column]]\n msidata = msidata[,pixelsofinterest]\n }else{\n+ msidata = msidata[,0]\n validpixels=0\n }\n \n- #else\n- validpixels=0\n- numberpixels = 0\n- #end if \n+\n+### Pixels in two columns format: x and y in different columns\n \n #elif str($pixels_cond.pixel_filtering) == "two_columns":\n print("two columns")\n \n- #if $pixels_cond.two_columns_pixel:\n-\n input_list = read.delim("$pixels_cond.two_columns_pixel", header = FALSE, \n stringsAsFactors = FALSE)\n numberpixels = length(input_list[,$pixels_cond.pixel_column_x])\n@@ -132,11 +128,8 @@\n validpixels=0\n }\n \n- \n- #else\n- validpixels=0\n- numberpixels = 0\n- #end if \n+\n+### Pixels wihin x and y minima and maxima are kept: \n \n #elif str($pixels_cond.pixel_filtering) == "pixel_range":\n print("pixel range")\n'..b'uality_control"/>\n- <param name="inputmz" value="702"/>\n+ <param name="inputmz" value="1200"/>\n <param name="plusminus_dalton" value="0.25"/>\n </conditional>\n <param name="output_matrix" value="True"/>\n@@ -552,14 +548,14 @@\n </param>\n <conditional name="outputs">\n <param name="outputs_select" value="quality_control"/>\n- <param name="inputmz" value="702"/>\n+ <param name="inputmz" value="1200"/>\n <param name="plusminus_dalton" value="0.25"/>\n </conditional>\n <output name="filtering_qc" file="analyze75_filtered2.pdf" compare="sim_size" delta="20000"/>\n- <output name="msidata_filtered" file="analyze_originaloutput2.RData" compare="sim_size" />\n+ <output name="msidata_filtered" file="analyze_filteredoutside.RData" compare="sim_size" />\n </test>\n <test expect_num_outputs="2">\n- <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>\n+ <param name="infile" value="preprocessed.RData" ftype="rdata"/>\n <conditional name="outputs">\n <param name="outputs_select" value="no_quality_control"/>\n </conditional>\n@@ -571,16 +567,32 @@\n <help>\n <![CDATA[\n \n-This tool can filter three types of mass-spectrometry imaging files (see below) for pixels and features of interest. This can be used to keep only pixels in a regions of interest.\n-For filtering at least one valid pixel/feature is needed otherwise no filtering will be performed. It is recommended to use the filtering tool only for feature masses which have been extracted from the same dataset. If you have feature masses from dataset A and you want to use them to filter dataset B, first find the corresponding (closest) features in dataset B by using the tool "Join two files on column allowing a small difference". Afterwards use the corresponding feature masses from dataset B to filter dataset B. \n+Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_\n+\n+This tool provides provides options to filter (subset) pixels and masses of mass-spectrometry imaging data.\n \n Input data: 3 types of input data can be used:\n \n-- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_\n+- imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_\n - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)\n - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)\n \n-The output of this tool is a subsetted Cardinal "MSImageSet" with the variable name "msidata" saved as .RData. \n+Options:\n+\n+- pixel filtering: can use a tabular file containing x and y coordinates or by defining a range for x and y by hand\n+- mass filtering: can use a tabular file containing masses of interest or by defining a range for the mass values\n+\n+Output: \n+\n+- imzML file filtered for pixels and/or masses\n+- optional: pdf with heatmap showing the pixels that are left after filtering and plot of masses before and after filtering\n+- optional: intensity matrix as tabular file (intensities for masses in rows and pixel in columns)\n+\n+Tip: \n+\n+- It is recommended to use the filtering tool only for masses which have been extracted from the same dataset. If you have masses from dataset A and you want to use them to filter dataset B, first find the corresponding (closest) features in dataset B by using the tool "Join two files on column allowing a small difference". Afterwards use the corresponding feature masses from dataset A to filter dataset B. \n+\n+\n ]]>\n </help>\n <citations>\n' |
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| diff -r 98c101b19f3c -r 22db5eb94e50 test-data/analyze_matrix.tabular --- a/test-data/analyze_matrix.tabular Mon Apr 23 17:18:35 2018 -0400 +++ b/test-data/analyze_matrix.tabular Mon May 28 12:36:24 2018 -0400 |
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| @@ -1,102 +1,24 @@ - x = 1, y = 1 x = 3, y = 1 x = 1, y = 2 x = 3, y = 2 x = 1, y = 3 -701.317626953125 1 0 0 0 0 -701.333435058594 2 0 0 0 0 -701.349243164062 2 0 0 0 0 -701.365051269531 3 0 0 0 0 -701.380859375 1 1 0 0 0 -701.396667480469 1 0 1 0 0 -701.412475585938 2 0 0 0 0 -701.428283691406 5 0 0 0 0 -701.444091796875 6 0 0 0 0 -701.459899902344 2 0 0 0 0 -701.475708007812 1 1 0 0 0 -701.491516113281 1 0 0 0 0 -701.50732421875 1 1 0 0 0 -701.523132324219 0 0 0 0 0 -701.538940429688 1 1 0 0 0 -701.554748535156 1 0 0 0 1 -701.570617675781 1 0 0 0 0 -701.58642578125 1 0 0 0 0 -701.602233886719 1 0 0 0 0 -701.618041992188 0 1 0 0 0 -701.633850097656 1 1 0 0 1 -701.649658203125 0 1 0 0 0 -701.665466308594 1 1 0 1 1 -701.681274414062 1 2 0 0 0 -701.697082519531 0 0 0 0 1 -701.712890625 2 0 0 0 1 -701.728759765625 3 0 0 0 0 -701.744567871094 1 1 0 1 0 -701.760375976562 1 2 0 0 0 -701.776184082031 0 1 0 1 0 -701.7919921875 0 0 0 0 1 -701.807800292969 0 0 0 0 0 -701.823608398438 2 0 1 0 0 -701.839416503906 3 1 0 1 0 -701.855224609375 4 1 0 0 1 -701.87109375 3 0 0 1 0 -701.886901855469 1 0 0 0 0 -701.902709960938 1 1 0 1 0 -701.918518066406 3 0 0 0 0 -701.934326171875 3 0 0 1 0 -701.950134277344 4 1 0 1 0 -701.965942382812 6 1 0 2 1 -701.981811523438 5 0 0 1 0 -701.997619628906 1 0 0 0 0 -702.013427734375 1 0 0 0 0 -702.029235839844 0 0 0 0 1 -702.045043945312 0 1 0 0 0 -702.060852050781 1 0 0 0 0 -702.076721191406 0 0 0 0 0 -702.092529296875 0 0 0 1 1 -702.108337402344 1 0 1 0 0 -702.124145507812 1 0 2 0 0 -702.139953613281 1 0 0 0 1 -702.15576171875 2 0 0 0 1 -702.171630859375 0 0 0 1 1 -702.187438964844 0 0 0 0 0 -702.203247070312 0 0 0 0 0 -702.219055175781 1 1 0 1 0 -702.23486328125 1 0 1 0 0 -702.250732421875 0 1 0 0 0 -702.266540527344 0 0 0 0 0 -702.282348632812 2 0 0 1 0 -702.298156738281 4 1 0 1 0 -702.31396484375 7 1 0 0 0 -702.329833984375 5 0 0 0 0 -702.345642089844 3 0 0 0 0 -702.361450195312 2 0 0 0 0 -702.377258300781 2 1 0 0 0 -702.393127441406 2 1 0 0 1 -702.408935546875 1 0 0 1 0 -702.424743652344 1 0 0 0 0 -702.440551757812 1 0 0 0 0 -702.456420898438 0 0 0 0 0 -702.472229003906 0 1 0 0 0 -702.488037109375 0 2 0 0 1 -702.503845214844 1 2 1 1 0 -702.519714355469 1 1 1 0 0 -702.535522460938 0 0 0 0 0 -702.551330566406 2 0 0 0 0 -702.567138671875 3 0 0 1 0 -702.5830078125 4 0 0 1 0 -702.598815917969 1 1 0 1 0 -702.614624023438 2 1 0 0 0 -702.630432128906 2 1 0 0 0 -702.646301269531 2 0 1 1 1 -702.662109375 1 0 1 0 1 -702.677917480469 0 0 1 2 0 -702.693725585938 0 0 0 3 1 -702.709594726562 1 0 1 2 0 -702.725402832031 2 0 0 1 0 -702.7412109375 3 0 0 0 0 -702.757080078125 2 1 0 0 1 -702.772888183594 2 1 0 1 0 -702.788696289062 5 0 0 0 0 -702.804565429688 7 0 0 0 0 -702.820373535156 5 1 0 0 0 -702.836181640625 3 0 0 0 0 -702.851989746094 2 0 0 0 1 -702.867858886719 1 0 0 0 0 -702.883666992188 2 0 0 0 0 -702.899475097656 5 1 0 0 1 + x = 1, y = 1 x = 1, y = 2 x = 3, y = 2 x = 1, y = 3 +1201.3349609375 14 12 9 14 +1201.37634277344 17 21 11 20 +1201.45910644531 22 18 18 22 +1201.54187011719 16 18 20 29 +1201.62475585938 13 14 13 20 +1201.66613769531 13 14 11 18 +1201.70751953125 12 13 10 17 +1201.79028320312 12 11 9 17 +1201.873046875 10 12 8 13 +1201.99719238281 7 8 9 12 +1202.07995605469 8 12 6 9 +1202.12145996094 10 8 7 10 +1202.16284179688 11 10 8 9 +1202.20422363281 14 9 10 10 +1202.24560546875 9 12 9 13 +1202.32836914062 16 10 10 13 +1202.41125488281 18 13 10 15 +1202.49401855469 12 11 14 24 +1202.53540039062 16 13 15 19 +1202.57678222656 17 12 11 14 +1202.65966796875 12 9 10 13 +1202.74243164062 12 8 10 13 +1202.86669921875 9 8 10 11 |
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| diff -r 98c101b19f3c -r 22db5eb94e50 test-data/featuresofinterest2.tabular --- a/test-data/featuresofinterest2.tabular Mon Apr 23 17:18:35 2018 -0400 +++ b/test-data/featuresofinterest2.tabular Mon May 28 12:36:24 2018 -0400 |
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| @@ -1,101 +1,101 @@ -"m/z = 701.32" -"m/z = 701.33" -"m/z = 701.35" -"m/z = 701.37" -"m/z = 701.38" -"m/z = 701.4" -"m/z = 701.41" -"m/z = 701.43" -"m/z = 701.44" -"m/z = 701.46" -"m/z = 701.48" -"m/z = 701.49" -"m/z = 701.51" -"m/z = 701.52" -"m/z = 701.54" -"m/z = 701.55" -"m/z = 701.57" -"m/z = 701.59" -"m/z = 701.6" -"m/z = 701.62" -"m/z = 701.63" -"m/z = 701.65" -"m/z = 701.67" -"m/z = 701.68" -"m/z = 701.7" -"m/z = 701.71" -"m/z = 701.73" -"m/z = 701.74" -"m/z = 701.76" -"m/z = 701.78" -"m/z = 701.79" -"m/z = 701.81" -"m/z = 701.82" -"m/z = 701.84" -"m/z = 701.86" -"m/z = 701.87" -"m/z = 701.89" -"m/z = 701.9" -"m/z = 701.92" -"m/z = 701.93" -"m/z = 701.95" -"m/z = 701.97" -"m/z = 701.98" -"m/z = 702" -"m/z = 702.01" -"m/z = 702.03" -"m/z = 702.05" -"m/z = 702.06" -"m/z = 702.08" -"m/z = 702.09" -"m/z = 702.11" -"m/z = 702.12" -"m/z = 702.14" -"m/z = 702.16" -"m/z = 702.17" -"m/z = 702.19" -"m/z = 702.2" -"m/z = 702.22" -"m/z = 702.23" -"m/z = 702.25" -"m/z = 702.27" -"m/z = 702.28" -"m/z = 702.3" -"m/z = 702.31" -"m/z = 702.33" -"m/z = 702.35" -"m/z = 702.36" -"m/z = 702.38" -"m/z = 702.39" -"m/z = 702.41" -"m/z = 702.42" -"m/z = 702.44" -"m/z = 702.46" -"m/z = 702.47" -"m/z = 702.49" -"m/z = 702.5" -"m/z = 702.52" -"m/z = 702.54" -"m/z = 702.55" -"m/z = 702.57" -"m/z = 702.58" -"m/z = 702.6" -"m/z = 702.61" -"m/z = 702.63" -"m/z = 702.65" -"m/z = 702.66" -"m/z = 702.68" -"m/z = 702.69" -"m/z = 702.71" -"m/z = 702.73" -"m/z = 702.74" -"m/z = 702.76" -"m/z = 702.77" -"m/z = 702.79" -"m/z = 702.8" -"m/z = 702.82" -"m/z = 702.84" -"m/z = 702.85" -"m/z = 702.87" -"m/z = 702.88" -"m/z = 702.9" +"m/z = 1201.32" +"m/z = 1201.33" +"m/z = 1201.35" +"m/z = 1201.37" +"m/z = 1201.38" +"m/z = 1201.4" +"m/z = 1201.41" +"m/z = 1201.43" +"m/z = 1201.44" +"m/z = 1201.46" +"m/z = 1201.48" +"m/z = 1201.49" +"m/z = 1201.51" +"m/z = 1201.52" +"m/z = 1201.54" +"m/z = 1201.55" +"m/z = 1201.57" +"m/z = 1201.59" +"m/z = 1201.6" +"m/z = 1201.62" +"m/z = 1201.63" +"m/z = 1201.65" +"m/z = 1201.67" +"m/z = 1201.68" +"m/z = 1201.7" +"m/z = 1201.71" +"m/z = 1201.73" +"m/z = 1201.74" +"m/z = 1201.76" +"m/z = 1201.78" +"m/z = 1201.79" +"m/z = 1201.81" +"m/z = 1201.82" +"m/z = 1201.84" +"m/z = 1201.86" +"m/z = 1201.87" +"m/z = 1201.89" +"m/z = 1201.9" +"m/z = 1201.92" +"m/z = 1201.93" +"m/z = 1201.95" +"m/z = 1201.97" +"m/z = 1201.98" +"m/z = 1202" +"m/z = 1202.01" +"m/z = 1202.03" +"m/z = 1202.05" +"m/z = 1202.06" +"m/z = 1202.08" +"m/z = 1202.09" +"m/z = 1202.11" +"m/z = 1202.12" +"m/z = 1202.14" +"m/z = 1202.16" +"m/z = 1202.17" +"m/z = 1202.19" +"m/z = 1202.2" +"m/z = 1202.22" +"m/z = 1202.23" +"m/z = 1202.25" +"m/z = 1202.27" +"m/z = 1202.28" +"m/z = 1202.3" +"m/z = 1202.31" +"m/z = 1202.33" +"m/z = 1202.35" +"m/z = 1202.36" +"m/z = 1202.38" +"m/z = 1202.39" +"m/z = 1202.41" +"m/z = 1202.42" +"m/z = 1202.44" +"m/z = 1202.46" +"m/z = 1202.47" +"m/z = 1202.49" +"m/z = 1202.5" +"m/z = 1202.52" +"m/z = 1202.54" +"m/z = 1202.55" +"m/z = 1202.57" +"m/z = 1202.58" +"m/z = 1202.6" +"m/z = 1202.61" +"m/z = 1202.63" +"m/z = 1202.65" +"m/z = 1202.66" +"m/z = 1202.68" +"m/z = 1202.69" +"m/z = 1202.71" +"m/z = 1202.73" +"m/z = 1202.74" +"m/z = 1202.76" +"m/z = 1202.77" +"m/z = 1202.79" +"m/z = 1202.8" +"m/z = 1202.82" +"m/z = 1202.84" +"m/z = 1202.85" +"m/z = 1202.87" +"m/z = 1202.88" +"m/z = 1202.9" |
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| diff -r 98c101b19f3c -r 22db5eb94e50 test-data/imzml_matrix3.tabular --- a/test-data/imzml_matrix3.tabular Mon Apr 23 17:18:35 2018 -0400 +++ b/test-data/imzml_matrix3.tabular Mon May 28 12:36:24 2018 -0400 |
| b |
| b'@@ -1,4 +1,1203 @@\n \tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 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200\t0\t4.09929134548292e-06\t0\n 200.083343505859\t0\t0\t0\n 200.16667175293\t1.39386879816072e-09\t0\t0\n' |
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| diff -r 98c101b19f3c -r 22db5eb94e50 test-data/inputpixels2.tabular --- a/test-data/inputpixels2.tabular Mon Apr 23 17:18:35 2018 -0400 +++ b/test-data/inputpixels2.tabular Mon May 28 12:36:24 2018 -0400 |
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| @@ -2,4 +2,4 @@ x = 1, y = 2 x = 1, y = 3 x = 3, y = 2 -x = 3, y = 1 +x = 5, y = 1 |
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| diff -r 98c101b19f3c -r 22db5eb94e50 test-data/inputpixels_2column.tabular --- a/test-data/inputpixels_2column.tabular Mon Apr 23 17:18:35 2018 -0400 +++ b/test-data/inputpixels_2column.tabular Mon May 28 12:36:24 2018 -0400 |
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| @@ -3,4 +3,4 @@ 1 C 3 3 D 1 3 E 2 -3 F 3 +30 F 3 |
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| diff -r 98c101b19f3c -r 22db5eb94e50 test-data/inputpixels_2column_challenge.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpixels_2column_challenge.tabular Mon May 28 12:36:24 2018 -0400 |
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| @@ -0,0 +1,3 @@ +12 A 1 +13 B 23 + |
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| diff -r 98c101b19f3c -r 22db5eb94e50 test-data/preprocessed.RData |
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| Binary file test-data/preprocessed.RData has changed |
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| diff -r 98c101b19f3c -r 22db5eb94e50 test-data/preprocessing_results1.RData |
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| Binary file test-data/preprocessing_results1.RData has changed |
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| diff -r 98c101b19f3c -r 22db5eb94e50 test-data/rdata_matrix.tabular --- a/test-data/rdata_matrix.tabular Mon Apr 23 17:18:35 2018 -0400 +++ b/test-data/rdata_matrix.tabular Mon May 28 12:36:24 2018 -0400 |
| b |
| b'@@ -1,1204 +1,4 @@\n \tx = 1, y = 1\tx = 2, y = 1\tx = 3, y = 1\tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 2\tx = 1, y = 3\tx = 2, y = 3\tx = 3, y = 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| diff -r 98c101b19f3c -r 22db5eb94e50 test-data/rdata_notfiltered.RData |
| b |
| Binary file test-data/rdata_notfiltered.RData has changed |