| Previous changeset 0:9cbcf48bf60a (2018-04-24) Next changeset 2:00b6c61f5054 (2018-05-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_combine commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f |
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modified:
msi_combine.xml test-data/123_combined_QC.pdf test-data/12_combined_QC.pdf |
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added:
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 9cbcf48bf60a -r f3f6c32ab690 msi_combine.xml --- a/msi_combine.xml Tue Apr 24 13:22:48 2018 -0400 +++ b/msi_combine.xml Tue May 08 02:36:26 2018 -0400 |
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| b'@@ -1,20 +1,21 @@\n-<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.7.0.0">\n+<tool id="mass_spectrometry_imaging_combine" name="MSI combine" version="1.10.0.0">\n <description>\n combine several mass spectrometry imaging datasets into one\n </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-ggplot2</requirement>\n </requirements>\n <command detect_errors="exit_code">\n <![CDATA[\n #for $i, $infile in enumerate($infiles):\n #if $infile.ext == \'imzml\'\n- cp \'${infile.extra_files_path}/imzml\' infile_$i.imzML &&\n- cp \'${infile.extra_files_path}/ibd\' infile_$i.ibd &&\n+ ln -s \'${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_$i.hdr &&\n- cp \'${infile.extra_files_path}/img\' infile_$i.img &&\n- cp \'${infile.extra_files_path}/t2m\' infile_$i.t2m &&\n+ ln -s \'${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 \'$infile\' infile_${i}.RData &&\n #end if\n@@ -26,24 +27,37 @@\n </command>\n <configfiles>\n <configfile name="msi_combine"><![CDATA[\n-library(Cardinal)\n+#import re\n+################ load libraries, read rename and combine files #################\n \n-#if $coordinates_file:\n- input_list = read.delim("$coordinates_file", header = FALSE, \n+library(Cardinal)\n+library(ggplot2)\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 pixel_vector = numeric()\n+names_vector = character()\n+x_shifts = 0\n+y_shifts = 0\n+max_y = numeric()\n \n #set $msidata = []\n+#set $pixelcoords = []\n+#set $num_infiles = len($infiles)\n+\n #for $i, $infile in enumerate($infiles):\n \n #if $infile.ext == \'imzml\'\n- msidata_$i <- readMSIData(\'infile_${i}.imzML\')\n+ msidata_$i <- readImzML(\'infile_${i}\')\n sampleNames(msidata_$i) = "msidata"\n+ pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))\n #elif $infile.ext == \'analyze75\'\n- msidata_$i <- readMSIData(\'infile_${i}.hdr\')\n+ msidata_$i <- readAnalyze(\'infile_${i}\')\n sampleNames(msidata_$i) = "msidata"\n+ pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))\n #else\n loadRData <- function(fileName){\n #loads an RData file, and returns it\n@@ -52,53 +66,190 @@\n }\n msidata_$i = loadRData(\'infile_${i}.RData\')\n sampleNames(msidata_$i) = "msidata"\n+ pixelcoords_$i = cbind(coord(msidata_$i)[,1:2], rep($i+1,ncol(msidata_$i)))\n #end if\n+ colnames(pixelcoords_$i)[3] = "file_number"\n \n- #if $coordinates_file:\n- coord(msidata_$i)\\$x = coord(msidata_$i)\\$x + input_list[$i+1+$coordinates_header,$column_x]\n- coord(msidata_$i)\\$y = coord(msidata_$i)\\$y + input_list[$i+1+$coordinates_header,$column_y]\n- pixelnumber = ncol(msidata_$i)\n- pixel_vector = append(pixel_vector, rep(input_list[$i+1+$coordinates_header,$column_names],times=pixelnumber))\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_lis'..b'bel="Column with values for shift in y direction" type="data_column"/>\n+ <param name="column_names" data_ref="coordinates_file" label="Column with dataset names" type="data_column"/>\n+ </when>\n+ <when value="no_combine"/>\n+ </conditional>\n+ <param name="output_matrix" type="boolean" display="radio" label="Intensity matrix output"/>\n </inputs>\n <outputs>\n <data format="rdata" name="msidata_combined" label="Combined MSI data"/>\n@@ -125,6 +292,7 @@\n <tests>\n <test expect_num_outputs="3">\n <param name="infiles" value="msidata_1.RData,msidata_2.RData,msidata_3.RData" ftype="rdata"/>\n+ <param name="combine_method" value="xy_shifts"/>\n <param name="coordinates_file" ftype="tabular" value="xy_coordinates.tabular"/>\n <param name="column_x" value="1"/>\n <param name="column_y" value="2"/>\n@@ -136,15 +304,36 @@\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="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+ <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+ </test>\n </tests>\n <help>\n <![CDATA[\n-This tool can combine several mass-spectrometry imaging files. A prerequesite for the combination is that the m/z values are the same across all datasets. To achieve this use the filtering tool to get all datasets to the same m/z range and then use the binning function in the preprocessing tool to obtain the same bins for all dataset. The pixels on the other hand must be unique, therefore you should provide a number for the shift of x and y coordinates so that pixels of different datasets do not overlap.\n+This tool can combine several mass-spectrometry imaging files. \n+ 1) m/z values need to be the same across all datasets\n+ 2) pixels (defined by x and y coordinates) must be unique\n+\n+1) Same m/z values/axis can be achieved with the filtering tool to get all datasets to the same m/z range and afterwards binning in the preprocessing tool to obtain the same bins for all dataset. \n+2) The pixels (defined by x and y coordinates) must be unique across all datasets, therefore the option "Select the way you want to combine multiple files" is helpful:\n+\n+ - "automatic combination": files are arranged in a grid with a distance in x and y direction which can be given by the user\n+ - "no coordinates shift": this option can only be used if all pixels are unique across datasets\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. You will only get a pdf which shows the arrangement of the pixels (with or without additional xy shifts)\n \n Input data: 3 types of input data can be used:\n \n' |
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| diff -r 9cbcf48bf60a -r f3f6c32ab690 test-data/12_auto_combined_matrix.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/12_auto_combined_matrix.tabular Tue May 08 02:36:26 2018 -0400 |
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| b'@@ -0,0 +1,8400 @@\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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