| Previous changeset 0:f17d3f1a065f (2018-02-28) Next changeset 2:22db5eb94e50 (2018-05-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_filtering commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1 |
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modified:
msi_filtering.xml test-data/analyze_filtered.RData test-data/analyze_filtered.pdf test-data/analyze_originaloutput.RData test-data/imzml_filtered.RData test-data/imzml_filtered.pdf test-data/inputfeatures.tabular |
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added:
test-data/analyze75_filtered2.pdf test-data/analyze_originaloutput2.RData test-data/featuresofinterest5.tabular 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/inputcalibrantfile2.txt test-data/inputpixels_2column.tabular test-data/rdata_notfiltered.RData |
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| diff -r f17d3f1a065f -r 98c101b19f3c msi_filtering.xml --- a/msi_filtering.xml Wed Feb 28 14:02:21 2018 -0500 +++ b/msi_filtering.xml Mon Apr 23 17:18:35 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.7.0">\n+<tool id="mass_spectrometry_imaging_filtering" name="MSI filtering" version="1.7.0.1">\n <description>tool for filtering mass spectrometry imaging data</description>\n <requirements>\n <requirement type="package" version="1.7.0">bioconductor-cardinal</requirement>\n@@ -45,7 +45,7 @@\n \n ###################################### inputfile properties in numbers ######################\n \n-#if $outputs.outputs_select == "quality_control"\n+#if $outputs.outputs_select == "quality_control":\n ## Number of features (mz)\n maxfeatures = length(features(msidata))\n ## Range mz\n@@ -76,63 +76,159 @@\n \n \n ###################################### filtering of pixels ######################\n-#if $inputpixels:\n- input_list = read.delim("$inputpixels", header = FALSE, \n- na.strings=c("","NA", "#NUM!", "#ZAHL!"), stringsAsFactors = FALSE)\n- validpixels = input_list[,$pixel_column] %in% names(pixels(msidata))\n+\n+#if str($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+ validpixels = sum(valid_entries)\n+\n+ if (validpixels != 0)\n+ {\n+ pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[valid_entries,$pixels_cond.pixel_column]]\n+ msidata = msidata[,pixelsofinterest]\n+ }else{\n+ validpixels=0\n+ }\n+\n+ #else\n+ validpixels=0\n+ numberpixels = 0\n+ #end if \n+\n+#elif str($pixels_cond.pixel_filtering) == "two_columns":\n+ print("two columns")\n \n- if (validpixels != 0)\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[,$pixels_cond.pixel_column_x])\n+\n+ inputpixel_x = input_list[,$pixels_cond.pixel_column_x]\n+ inputpixel_y = input_list[,$pixels_cond.pixel_column_y]\n+\n+ inputpixels = cbind(inputpixel_x, inputpixel_y)\n+ colnames(inputpixels) = c("x", "y")\n+ valid_rows = merge(inputpixels, coord(msidata)[,1:2])\n+ validpixels = nrow(valid_rows)\n+\n+ if (validpixels != 0)\n {\n- pixelsofinterest = pixels(msidata)[names(pixels(msidata)) %in% input_list[validpixels,$pixel_column]]\n+\n+ pixelvector = character()\n+\n+ for (pixel in 1:nrow(valid_rows))\n+ {\n+ pixelvector[pixel] = paste0("x = ", valid_rows[pixel,1],", ", "y = ", valid_rows[pixel,2])\n+ }\n+\n+ pixelsofinterest= pixels(msidata)[names(pixels(msidata)) %in% pixelvector]\n msidata = msidata[,pixelsofinterest]\n- numberpixels = length(input_list[,$pixel_column])\n- }else {\n- numberpixels = 0\n+ }else{\n+ validpixels=0\n }\n \n+ \n+ #else\n+ validpixels=0\n+ numberpixels = 0\n+ #end if \n \n-#else\n- input_list = data.frame(0, 0)\n- validpixels=0\n+#elif str($pixels_cond.pixel_filtering) == "pixel_range":\n+ print("pixel range")\n+\n+ numberpixels = "range"\n+ validpixels = "range"\n+\n+ if (sum(coord(msidata)\\$x <= $pixels_cond.max_x_range & coord(msidata)\\$x >= $pixels_cond.min_x_range) > 0)\n+ {\n+ msidata = msidata[, coord(msidata)\\$x <= $pixels_cond.max_x_range & coord(msidata)\\$x >= $pixels_cond.min_x_range]\n+ }\n+\n+ if (sum(coord(msidata)\\$y <= $pixels_cond.max_y_range & coord(msidata)\\$y >= $pixels_cond.min_y_range) > 0)\n+ {\n+ msidata = msidata[, coord(msidata)\\$y <= $pixels_cond.max_y_range & coord(msida'..b'aram name="max_y_range" value="20"/>\n+ <param name="features_filtering" value="features_range"/>\n+ <param name="min_mz" value="1" />\n+ <param name="max_mz" value="150"/>\n+ <param name="outputs_select" value="quality_control"/>\n+ <param name="inputmz" value="328.9"/>\n+ <param name="plusminus_dalton" value="0.25"/>\n+ <output name="filtering_qc" file="imzml_filtered5.pdf" compare="sim_size" delta="20000"/>\n+ <output name="msidata_filtered" file="imzml_filtered5.RData" compare="sim_size" />\n+ </test>\n <test expect_num_outputs="3">\n <param name="infile" value="" ftype="analyze75">\n <composite_data value="Analyze75.hdr"/>\n <composite_data value="Analyze75.img"/>\n <composite_data value="Analyze75.t2m"/>\n </param>\n- <param name="inputpixels" ftype="tabular" value = "inputpixels2.tabular"/>\n+ <param name="pixel_filtering" value="single_column"/>\n+ <param name="single_pixels" ftype="tabular" value = "inputpixels2.tabular"/>\n <param name="pixel_column" value="1"/>\n+ <param name="features_filtering" value="features_list"/>\n <param name="inputfeatures" ftype="tabular" value = "featuresofinterest2.tabular"/>\n <param name="feature_column" value="1"/>\n <conditional name="outputs">\n@@ -320,16 +544,19 @@\n <output name="msidata_filtered" file="analyze_filtered.RData" compare="sim_size" />\n <output name="matrixasoutput" file="analyze_matrix.tabular"/>\n </test>\n- <test expect_num_outputs="1">\n+ <test expect_num_outputs="2">\n <param name="infile" value="" ftype="analyze75">\n <composite_data value="Analyze75.hdr"/>\n <composite_data value="Analyze75.img"/>\n <composite_data value="Analyze75.t2m"/>\n </param>\n <conditional name="outputs">\n- <param name="outputs_select" value="no_quality_control"/>\n+ <param name="outputs_select" value="quality_control"/>\n+ <param name="inputmz" value="702"/>\n+ <param name="plusminus_dalton" value="0.25"/>\n </conditional>\n- <output name="msidata_filtered" file="analyze_originaloutput.RData" compare="sim_size" />\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 </test>\n <test expect_num_outputs="2">\n <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>\n@@ -338,13 +565,14 @@\n </conditional>\n <param name="output_matrix" value="True"/>\n <output name="matrixasoutput" file="rdata_matrix.tabular"/>\n+ <output name="msidata_filtered" file="rdata_notfiltered.RData" compare="sim_size" />\n </test>\n </tests>\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.\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 \n Input data: 3 types of input data can be used:\n \n' |
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| @@ -0,0 +1,101 @@ +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 +115.583335876465 +115.666664123535 +115.75 +115.833335876465 +115.916664123535 +116 +116.083335876465 +116.166664123535 +116.25 +116.333335876465 +116.416664123535 +116.5 +116.583335876465 +116.666664123535 |
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| diff -r f17d3f1a065f -r 98c101b19f3c test-data/imzml_matrix3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/imzml_matrix3.tabular Mon Apr 23 17:18:35 2018 -0400 |
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| b'@@ -0,0 +1,3602 @@\n+\tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 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|
| b |
| diff -r f17d3f1a065f -r 98c101b19f3c test-data/inputcalibrantfile2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputcalibrantfile2.txt Mon Apr 23 17:18:35 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +869.51 mass1 +1001.62 mass2 +1023.6 mass3 |
| b |
| diff -r f17d3f1a065f -r 98c101b19f3c test-data/inputfeatures.tabular --- a/test-data/inputfeatures.tabular Wed Feb 28 14:02:21 2018 -0500 +++ b/test-data/inputfeatures.tabular Mon Apr 23 17:18:35 2018 -0400 |
| b |
| @@ -1,3 +1,4 @@ +nothing here features here m/z = 100.08 m/z = 100.17 m/z = 100.25 |
| b |
| diff -r f17d3f1a065f -r 98c101b19f3c test-data/inputpixels_2column.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputpixels_2column.tabular Mon Apr 23 17:18:35 2018 -0400 |
| b |
| @@ -0,0 +1,6 @@ +1 A 1 +1 B 2 +1 C 3 +3 D 1 +3 E 2 +3 F 3 |
| b |
| diff -r f17d3f1a065f -r 98c101b19f3c test-data/rdata_notfiltered.RData |
| b |
| Binary file test-data/rdata_notfiltered.RData has changed |