| Previous changeset 2:22db5eb94e50 (2018-05-28) Next changeset 4:bf61fc662615 (2018-06-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit a7be47698f53eb4f00961192327d93e8989276a7 |
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modified:
msi_filtering.xml test-data/Example_Continuous.ibd test-data/Example_Continuous.imzML test-data/analyze75_filtered2.pdf test-data/analyze_filtered.RData test-data/analyze_filtered.pdf test-data/analyze_filteredoutside.RData test-data/featuresofinterest5.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 |
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| diff -r 22db5eb94e50 -r d51c3c814d57 msi_filtering.xml --- a/msi_filtering.xml Mon May 28 12:36:24 2018 -0400 +++ b/msi_filtering.xml Mon Jun 11 17:33:40 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.0">\n+<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.10.0.1">\n <description>tool for filtering mass spectrometry imaging data</description>\n <requirements>\n <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>\n@@ -41,12 +41,13 @@\n load(\'infile.RData\')\n #end if\n \n-##################################### QC: inputfile properties in numbers ######\n+########################### optional QC numbers ########################\n \n #if $outputs.outputs_select == "quality_control":\n- ## Number of features (mz)\n+\n+ ## Number of features (m/z)\n maxfeatures = length(features(msidata))\n- ## Range mz\n+ ## Range m/z\n minmz = round(min(mz(msidata)), digits=2)\n maxmz = round(max(mz(msidata)), digits=2)\n ## Number of spectra (pixels)\n@@ -59,7 +60,7 @@\n maximumy = max(coord(msidata)[,2])\n ## Number of intensities > 0\n npeaks= sum(spectra(msidata)[]>0)\n- ## Spectra multiplied with mz (potential number of peaks)\n+ ## Spectra multiplied with m/z (potential number of peaks)\n numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])\n ## Percentage of intensities > 0\n percpeaks = round(npeaks/numpeaks*100, digits=2)\n@@ -70,66 +71,55 @@\n medint = round(median(TICs), digits=2)\n ## Store features for QC plot\n featuresinfile = mz(msidata)\n+\n #end if\n \n+###################################### Filtering of pixels #####################\n+################################################################################\n \n-###################################### Filtering of pixels #####################\n-\n-### Pixels in the one column format "x=,y="\n+#################### Pixels in the one column format "x=,y=" #####################\n \n #if str($pixels_cond.pixel_filtering) == "single_column":\n print("single column")\n \n- 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[,$pixels_cond.pixel_column] %in% names(pixels(msidata))\n- validpixels = sum(valid_entries)\n+ input_list = read.delim("$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+ validpixels = sum(valid_entries)\n \n- if (validpixels != 0)\n- {\n- pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[valid_entries,$pixels_cond.pixel_column]]\n- msidata = msidata[,pixelsofinterest]\n- }else{\n- msidata = msidata[,0]\n- validpixels=0\n- }\n+ if (validpixels != 0){\n+ pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[valid_entries,$pixels_cond.pixel_column]]\n+ msidata = msidata[,pixelsofinterest]\n+ }else{\n+ msidata = msidata[,0]\n+ validpixels=0}\n \n-\n-### Pixels in two columns format: x and y in different columns\n+############ Pixels in two columns format: x and y in different columns #############\n \n #elif str($pixels_cond.pixel_filtering) == "two_columns":\n print("two columns")\n \n- input_list = read.delim("$pixels_cond.two_columns_pixel", header = FALSE, \n- stringsAsFactors = FALSE)\n- numberpixels = length(input_list[,$pixels_cond.pixel_column_x])\n-\n- inputpixel_x = input_list[,$pixels_cond.pixel_column_x]\n- inputpixel_y = input_list[,$pixels_cond.pixel_column_y]\n+ input_list = read.delim("$pixels_cond.two_columns_pixel", header = FALSE, \n+ stringsAsFactors = FALSE)\n+ numberpixels = length(input_list[,$pixels_cond.pixel_column_x])\n \n- inputpixels = cbind(inputpixel_x, inputpixel_y)\n- colna'..b' </data>\n </outputs>\n@@ -470,7 +484,7 @@\n <param name="min_y_range" value="2"/>\n <param name="max_y_range" value="2"/>\n <param name="features_filtering" value="features_range"/>\n- <param name="min_mz" value="0" />\n+ <param name="min_mz" value="350" />\n <param name="max_mz" value="500"/>\n <param name="outputs_select" value="quality_control"/>\n <param name="inputmz" value="328.9"/>\n@@ -509,9 +523,10 @@\n <param name="max_x_range" value="10"/>\n <param name="min_y_range" value="2"/>\n <param name="max_y_range" value="20"/>\n- <param name="features_filtering" value="features_range"/>\n- <param name="min_mz" value="500" />\n- <param name="max_mz" value="700"/>\n+ <param name="features_filtering" value="features_list"/>\n+ <param name="inputfeatures" ftype="tabular" value = "featuresofinterest5.tabular"/>\n+ <param name="feature_column" value="1"/>\n+ <param name="feature_header" value="0"/>\n <param name="outputs_select" value="quality_control"/>\n <param name="inputmz" value="328.9"/>\n <param name="plusminus_dalton" value="0.25"/>\n@@ -569,7 +584,7 @@\n \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+This tool provides provides options to filter (subset) pixels and m/z features of mass spectrometry imaging data.\n \n Input data: 3 types of input data can be used:\n \n@@ -577,20 +592,24 @@\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+\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+- m/z feature filtering: can use a tabular file containing m/z of interest or by defining a range for the m/z values (! numeric input will be rounded to 2 digits before matching to m/z!)\n+- m/z feature removing: infering m/z such as matrix contaminants can be removed by specifying their m/z in a tabular file and optionally set a window (window in ppm or Da in which peaks should be removed)\n+\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+- imzML file filtered for pixels and/or m/z\n+- optional: pdf with heatmap showing the pixels that are left after filtering and plot of m/z before and after filtering\n+- optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)\n+\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+- It is recommended to use the filtering tool only for m/z which have been extracted from the same dataset. If you have m/z 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 m/z from dataset A to filter dataset B. \n \n \n ]]>\n' |
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| b'@@ -1,373 +1,313 @@\n-<?xml version="1.0" encoding="ISO-8859-1"?>\r\n-<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd" version="1.1">\r\n- <cvList count="3">\r\n- <cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo"/>\r\n- <cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\r\n- <cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo"/>\r\n- </cvList>\r\n- <fileDescription>\r\n- <fileContent>\r\n- <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value=""/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{554A27FA-79D2-4766-9A2C-862E6D78B1F3}"/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="A5BE532D25997B71BE6D20C76561DDC4D5307DDD"/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value=""/>\r\n- </fileContent>\r\n- <sourceFileList count="1">\r\n- <sourceFile id="sf1" name="Example.raw" location="C:\\Users\\Thorsten Schramm\\Documents\\Promotion\\imzML\\Website\\files\\Beispiel-Dateien\\Example images\\">\r\n- <cvParam cvRef="MS" accession="MS:1000563" name="Thermo RAW file" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000768" name="Thermo nativeID format" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="7623BE263B25FF99FDF017154B86FAB742D4BB0B"/>\r\n- </sourceFile>\r\n- </sourceFileList>\r\n- <contact>\r\n- <cvParam cvRef="MS" accession="MS:1000586" name="contact name" value="Thorsten Schramm"/>\r\n- <cvParam cvRef="MS" accession="MS:1000590" name="contact organization" value="Institut f\xfcr Anorganische und Analytische Chemie"/>\r\n- <cvParam cvRef="MS" accession="MS:1000587" name="contact address" value="Schubertstra\xdfe 60, Haus 16, Gie\xdfen, Germany"/>\r\n- <cvParam cvRef="MS" accession="MS:1000589" name="contact email" value="thorsten.schramm@anorg.chemie.uni-.giessen.de"/>\r\n- </contact>\r\n- </fileDescription>\r\n- <referenceableParamGroupList count="4">\r\n- <referenceableParamGroup id="mzArray">\r\n- <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z"/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\r\n- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>\r\n- </referenceableParamGroup>\r\n- <referenceableParamGroup id="intensityArray">\r\n- <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>\r\n- <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true"/>\r\n- <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value=""/>\r\n- </referenceableParamGroup>\r\n- <referenceableParamGroup id="scan1">\r\n- <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000095" name="linear" value=""/>\r\n- <cvParam cvRef="MS" accession="MS:1000512" name="filter string" value="ITMS - 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| @@ -1,87 +1,3 @@ -108.333335876465 -108.416664123535 -108.5 -108.583335876465 -108.666664123535 -108.75 -108.833335876465 -108.916664123535 -109 -109.083335876465 -109.166664123535 -109.25 -109.333335876465 -109.416664123535 -109.5 -109.583335876465 -109.666664123535 -109.75 -109.833335876465 -109.916664123535 -110 -110.083335876465 -110.166664123535 -110.25 -110.333335876465 -110.416664123535 -110.5 -110.583335876465 -110.666664123535 -110.75 -110.833335876465 -110.916664123535 -111 -111.083335876465 -111.166664123535 -111.25 -111.333335876465 -111.416664123535 -111.5 -111.583335876465 -111.666664123535 -111.75 -111.833335876465 -111.916664123535 -112 -112.083335876465 -112.166664123535 -112.25 -112.333335876465 -112.416664123535 -112.5 -112.583335876465 -112.666664123535 -112.75 -112.833335876465 -112.916664123535 -113 -113.083335876465 -113.166664123535 -113.25 -113.333335876465 -113.416664123535 -113.5 -113.583335876465 -113.666664123535 -113.75 -113.833335876465 -113.916664123535 -114 -114.083335876465 -114.166664123535 -114.25 -114.333335876465 -114.416664123535 -114.5 -114.583335876465 -114.666664123535 -114.75 -114.833335876465 -114.916664123535 -115 -115.083335876465 -115.166664123535 -115.25 115.333335876465 115.416664123535 115.5 @@ -99,3 +15,17 @@ 116.5 116.583335876465 116.666664123535 +319.083343505859 +319.166687011719 +319.25 +319.333343505859 +319.416687011719 +319.5 +319.583343505859 +319.666687011719 +319.75 +319.8 +319.916687011719 +320 +320.0833435 +350 |
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| Binary file test-data/imzml_filtered5.pdf has changed |
| b |
| diff -r 22db5eb94e50 -r d51c3c814d57 test-data/imzml_matrix3.tabular --- a/test-data/imzml_matrix3.tabular Mon May 28 12:36:24 2018 -0400 +++ b/test-data/imzml_matrix3.tabular Mon Jun 11 17:33:40 2018 -0400 |
| b |
| b'@@ -1,3003 +1,4 @@\n \tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 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|