| Previous changeset 2:00b6c61f5054 (2018-05-28) Next changeset 4:d05bd881af3d (2018-06-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit a7be47698f53eb4f00961192327d93e8989276a7 |
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modified:
msi_combine.xml test-data/123_combined.RData test-data/123_combined_QC.pdf test-data/12_combined.RData test-data/12_combined_QC.pdf test-data/12_combined_matrix.tabular |
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added:
test-data/112_auto_combined.RData test-data/112_auto_combined_QC.pdf test-data/123_no_combi.RData test-data/123_no_combi_QC.pdf |
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removed:
test-data/12_auto_combined.RData test-data/12_auto_combined_QC.pdf test-data/12_auto_combined_matrix.tabular |
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| diff -r 00b6c61f5054 -r 91bba2486773 msi_combine.xml --- a/msi_combine.xml Mon May 28 12:35:49 2018 -0400 +++ b/msi_combine.xml Mon Jun 11 17:33:28 2018 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.0">\n+<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.1">\n <description>\n combine several mass spectrometry imaging datasets into one\n </description>\n@@ -10,12 +10,12 @@\n <![CDATA[\n #for $i, $infile in enumerate($infiles):\n #if $infile.ext == \'imzml\'\n- ln -s \'${infile.extra_files_path}/imzml\' infile.imzML &&\n- ln -s \'${infile.extra_files_path}/ibd\' infile.ibd &&\n+ ln -s \'${infile.extra_files_path}/imzml\' infile_${i}.imzML &&\n+ ln -s \'${infile.extra_files_path}/ibd\' infile_${i}.ibd &&\n #elif $infile.ext == \'analyze75\'\n- ln -s \'${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+ ln -s \'${infile.extra_files_path}/hdr\' infile_${i}.hdr &&\n+ ln -s \'${infile.extra_files_path}/img\' infile_${i}.img &&\n+ ln -s \'${infile.extra_files_path}/t2m\' infile_${i}.t2m &&\n #else\n ln -s \'$infile\' infile_${i}.RData &&\n #end if\n@@ -27,34 +27,44 @@\n </command>\n <configfiles>\n <configfile name="msi_combine"><![CDATA[\n+\n #import re\n-################ load libraries, read rename and combine files #################\n+\n+################ load libraries and some preparations #################\n \n library(Cardinal)\n library(ggplot2)\n \n+## read tabular file for xy_shift option\n+\n #if str( $combine_conditional.combine_method ) == \'xy_shifts\':\n input_list = read.delim("$combine_conditional.coordinates_file", header = FALSE, \n stringsAsFactors = FALSE)\n #end if\n \n+## load RData and store with new variable name\n+\n loadRData <- function(fileName){\n #loads an RData file, and returns it\n load(fileName)\n get(ls()[ls() != "fileName"])\n }\n \n+## preparations for reading files one by one with for loop\n+\n pixel_vector = numeric()\n-names_vector = character()\n x_shifts = 0\n y_shifts = 0\n max_y = numeric()\n-\n+valid_dataset = logical()\n #set $msidata = []\n #set $pixelcoords = []\n #set $num_infiles = len($infiles)\n all_files = $num_infiles\n \n+\n+############## reading files and changing pixel coordinates ###################\n+\n #for $i, $infile in enumerate($infiles):\n \n #if $infile.ext == \'imzml\'\n@@ -63,56 +73,79 @@\n msidata_$i <- readAnalyze(\'infile_${i}\')\n #else\n msidata_$i = loadRData(\'infile_${i}.RData\')\n- #end if\n+ #end if\n \n-########## wenn ncol msidata > 0 and nrow msidata > 0, dann alles abklappern andernfalls nicht in msiliste mitreinnehmen (unten hinter python vor end for: filenr ausprinten)\n- sampleNames(msidata_$i) = "msidata"\n- pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))\n+ sampleNames(msidata_$i) = "msidata" ## same name necessary to combine data in one single coordinate system\n+\n+ ################### preparation xy shifts ##########################\n \n #if str( $combine_conditional.combine_method ) == \'xy_shifts\':\n- coord(msidata_$i)\\$x = coord(msidata_$i)\\$x + input_list[$i+1,$combine_conditional.column_x]\n- coord(msidata_$i)\\$y = coord(msidata_$i)\\$y + input_list[$i+1,$combine_conditional.column_y]\n- pixel_vector = append(pixel_vector, rep(input_list[$i+1,$combine_conditional.column_names],times=ncol(msidata_$i)))\n- \n+\n+ coord(msidata_$i)\\$x = coord(msidata_$i)\\$x + input_list[$i+1,$combine_conditional.column_x] ## shifts x coordinates according to tabular file\n+ coord(msidata_$i)\\$y = coord(msidata_$i)\\$y + input_list[$i+1,$combine_conditional.column_y] ## shifts y coordinates according to tabular file\n+ pixel_vector = append(pixel_vector, rep(paste($i+1, input_list[$i+1,$combine_conditional.column_names], sep="_"),times=ncol(msidata_$i))) #'..b'/>\n+ <param name="combination_true" value="no_combi"/>\n+ <output name="msidata_combined" file="123_no_combi.RData" compare="sim_size" />\n+ <output name="combining_qc" file="123_no_combi_QC.pdf" compare="sim_size" delta="20000"/>\n+ </test>\n <test expect_num_outputs="3">\n <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>\n- <param name="combine_method" value="no_shifts"/>\n+ <param name="combine_method" value="automatic_combine"/>\n <param name="output_matrix" value="True"/>\n <output name="matrixasoutput" file="12_combined_matrix.tabular"/>\n <output name="msidata_combined" file="12_combined.RData" compare="sim_size" />\n <output name="combining_qc" file="12_combined_QC.pdf" compare="sim_size" delta="20000"/>\n </test>\n- <test expect_num_outputs="3">\n- <param name="infiles" value="msidata_1.RData,msidata_2.RData" ftype="rdata"/>\n+ <test expect_num_outputs="2">\n+ <param name="infiles" value="msidata_1.RData,123_combined.RData" ftype="rdata"/>\n <param name="combine_method" value="automatic_combine"/>\n- <param name="x_distance" value="1"/>\n- <param name="y_distance" value="1"/>\n- <param name="output_matrix" value="True"/>\n- <output name="matrixasoutput" file="12_auto_combined_matrix.tabular"/>\n- <output name="msidata_combined" file="12_auto_combined.RData" compare="sim_size" />\n- <output name="combining_qc" file="12_auto_combined_QC.pdf" compare="sim_size" delta="20000"/>\n+ <param name="output_matrix" value="False"/>\n+ <output name="msidata_combined" file="112_auto_combined.RData" compare="sim_size" />\n+ <output name="combining_qc" file="112_auto_combined_QC.pdf" compare="sim_size" delta="20000"/>\n </test>\n </tests>\n <help>\n@@ -329,7 +311,7 @@\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 uses the Cardinal combine function to combine several mass-spectrometry imaging data. \n+This tool uses the Cardinal combine function to combine several mass spectrometry imaging data. \n \n Input data: 3 types of input data can be used:\n \n@@ -343,16 +325,15 @@\n \n Options: \n \n-- "automatic combination": files are arranged in a grid with a minimal distance in x and y direction which can be given by the user, subfiles are named according to input file name\n-- "no coordinates shift": this option can only be used if all pixels are unique across datasets, no assignment of names to the subfiles\n-- "xy shifts by hand": each file can be moved in x and y direction according to the users need (define one tabular file in the order in which the files are loaded in the history (bottom to top) and define for each file the x and y coordinates shifts in separate columns\n-- "check pixels before combination": no combination takes place but a pdf shows the current arrangement of the pixels\n+- "automatic combination": files are automatically arranged in a grid, subfiles are named according to input file name\n+- "xy shifts by hand": each file can be moved in x and y direction according to the users need (define one tabular file in the order in which the files are loaded in the history (bottom to top) and define for each file the x and y coordinates shifts in separate columns and the file name in a third column). To test if the pixels are correctly shifted use "combine datasets: No".\n+\n \n Output: \n \n - imzML file containing multiple subfiles\n - pdf that shows the pixel positions of the combined files\n-- optional: intensity matrix as tabular file (intensities for masses in rows and pixel in columns)\n+- optional: intensity matrix as tabular file (intensities for m/z in rows and pixel in columns)\n \n \n ]]>\n' |
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| diff -r 00b6c61f5054 -r 91bba2486773 test-data/12_auto_combined_matrix.tabular --- a/test-data/12_auto_combined_matrix.tabular Mon May 28 12:35:49 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,8400 +0,0 @@\n-\tx = 1, y = 1\tx = 1, y = 2\tx = 1, y = 3\tx = 3, y = 1\tx = 4, y = 1\tx = 3, y = 2\tx = 4, y = 2\tx = 3, y = 3\tx = 4, y = 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| diff -r 00b6c61f5054 -r 91bba2486773 test-data/12_combined.RData |
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| Binary file test-data/12_combined.RData has changed |
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| diff -r 00b6c61f5054 -r 91bba2486773 test-data/12_combined_QC.pdf |
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| diff -r 00b6c61f5054 -r 91bba2486773 test-data/12_combined_matrix.tabular --- a/test-data/12_combined_matrix.tabular Mon May 28 12:35:49 2018 -0400 +++ b/test-data/12_combined_matrix.tabular Mon Jun 11 17:33:28 2018 -0400 |
| b |
| @@ -1,4 +1,4 @@ - x = 1, y = 1 x = 1, y = 2 x = 1, y = 3 x = 2, y = 1 x = 3, y = 1 x = 2, y = 2 x = 3, y = 2 x = 2, y = 3 x = 3, y = 3 + x = 1, y = 1 x = 1, y = 2 x = 1, y = 3 x = 7, y = 1 x = 8, y = 1 x = 7, y = 2 x = 8, y = 2 x = 7, y = 3 x = 8, y = 3 100.083335876465 0 0 0 0 0 0 0 0 0 100.166664123535 0 0 0 0 0 0 0 0 0 100.25 0 0 0 0 0 0 0 0 0 |