| Previous changeset 4:48c07268f341 (2019-03-22) Next changeset 6:bb1ac6b47a6c (2020-03-25) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 1df4591de435d232862f20669aea529ceb23b12a" |
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modified:
combine.xml test-data/112_annotation_output.tabular test-data/112_auto_combined.ibd test-data/112_auto_combined.imzml test-data/112_auto_combined.imzml.txt test-data/112_auto_combined_QC.pdf test-data/123_annotation_output.tabular test-data/123_combined.RData test-data/123_combined_QC.pdf test-data/123_combined_auto.ibd test-data/123_combined_auto.imzml test-data/123_combined_auto.imzml.txt test-data/123_combined_auto.pdf test-data/12_annotation_output.tabular test-data/12_combined_QC.pdf test-data/2123_auto_combined_QC.pdf |
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added:
test-data/123_combine.rdata test-data/123_combined.ibd test-data/123_combined.imzml test-data/123_combined.imzml.txt test-data/123_combined_picked.rdata test-data/123_combined_picked2.rdata test-data/12_combined.ibd test-data/12_combined.imzml test-data/12_combined.imzml.txt test-data/2123_auto_combined.ibd test-data/2123_auto_combined.imzml test-data/2123_auto_combined.imzml.txt test-data/picked.ibd test-data/picked.imzml test-data/picked.imzml.txt test-data/picked.tabular test-data/picked_QC.pdf test-data/xy_coordinates2.tabular |
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removed:
test-data/12_combined.RData test-data/2123_auto_combined.RData |
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| diff -r 48c07268f341 -r b41107d8fe89 combine.xml --- a/combine.xml Fri Mar 22 08:18:29 2019 -0400 +++ b/combine.xml Fri Dec 13 13:54:23 2019 -0500 |
| [ |
| b'@@ -1,13 +1,17 @@\n-<tool id="cardinal_combine" name="MSI combine" version="@VERSION@.3">\n+<tool id="cardinal_combine" name="MSI combine" version="2.2.6.0">\n <description>\n combine several mass spectrometry imaging datasets into one\n </description>\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro="requirements">\n- <requirement type="package" version="3.0">r-ggplot2</requirement>\n- </expand>\n+ <requirements>\n+ <requirement type="package" version="2.2.6">bioconductor-cardinal</requirement>\n+ <requirement type="package" version="3.6.1">r-base</requirement>\n+ <requirement type="package" version="3.2.1">r-ggplot2</requirement>\n+ <requirement type="package" version="0.12">r-maldiquantforeign</requirement>\n+ <requirement type="package" version="1.19.3">r-maldiquant</requirement>\n+ </requirements>\n <command detect_errors="exit_code">\n <![CDATA[\n #for $i, $infile in enumerate($infiles):\n@@ -30,11 +34,9 @@\n \n cat \'${msi_combine}\' &&\n Rscript \'${msi_combine}\' &&\n- #if str($imzml_output) == "imzml_format":\n- mkdir $outfile_imzml.files_path &&\n- mv ./out.imzML "${os.path.join($outfile_imzml.files_path, \'imzml\')}" | true &&\n- mv ./out.ibd "${os.path.join($outfile_imzml.files_path, \'ibd\')}" | true &&\n- #end if\n+ mkdir $outfile_imzml.files_path &&\n+ mv ./out.imzML "${os.path.join($outfile_imzml.files_path, \'imzml\')}" | true &&\n+ mv ./out.ibd "${os.path.join($outfile_imzml.files_path, \'ibd\')}" | true &&\n echo "imzML file:" > $outfile_imzml &&\n ls -l "$outfile_imzml.files_path" >> $outfile_imzml\n \n@@ -42,13 +44,14 @@\n </command>\n <configfiles>\n <configfile name="msi_combine"><![CDATA[\n-\n #import re\n \n-################ load libraries and some preparations #################\n+################ 1) load libraries and do preparations #################\n \n library(Cardinal)\n library(ggplot2)\n+library(MALDIquantForeign)\n+library(MALDIquant)\n \n ## read tabular file for xy_shift option\n #if str( $combine_conditional.combine_method ) == \'xy_shifts\':\n@@ -63,18 +66,19 @@\n }\n \n ## preparations for reading files one by one with for loop\n-pixel_vector = numeric()\n+sample_names = numeric()\n x_shifts = 0\n y_shifts = 0\n max_y = numeric()\n valid_dataset = logical()\n+coordinates_combined = data.frame(matrix(,ncol=2, nrow=0))\n+msidata_combined = list()\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+###################### 2) reading MSI files ####################################\n \n #for $i, $infile in enumerate($infiles):\n \n@@ -82,197 +86,226 @@\n \n #if $infile.ext == \'imzml\'\n #if str($processed_cond.processed_file) == "processed":\n- msidata_$i <- readImzML(\'infile_${i}\', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE)\n+ msidata_$i <- readImzML(\'infile_${i}\', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units", attach.only=TRUE, as = c("MSImageSet"))\n centroided(msidata_$i) = $centroids\n #else\n- msidata_$i <- readImzML(\'infile_${i}\', attach.only=TRUE)\n+ msidata_$i <- readImzML(\'infile_${i}\', attach.only=TRUE, as = c("MSImageSet"))\n centroided(msidata_$i) = $centroids\n #end if\n #elif $infile.ext == \'analyze75\'\n- msidata_$i <- readAnalyze(\'infile_${i}\', attach.only=TRUE)\n+ msidata_$i <- readAnalyze(\'infile_${i}\', attach.only=TRUE, as = c("MSImageSet"))\n centroided(msidata_$i) = $centroids\n #else\n msidata_$i = loadRData(\'infile_${i}.RData\')\n+ ## keep compatibility with old .RData files:\n+ msidata_$i\\$column1 = NULL\n+ msidata_$i\\$column2 = NUL'..b've about the same pixel dimensions which is smaller than 510x260.\n- - The file can have any column names as header (in this case set "Tabular file contains a header line" to yes) or no header at all\n+ - Each input file is renamed and shifted in x and y direction according to this tabular file. In the example the files have about the same pixel dimensions which is smaller than 510x260.\n+ - The file can have any column names as header (in this case set "Tabular file contains a header line" to "Yes") or no header at all (set "Tabular file contains a header line" to "No").\n \n ::\n \n@@ -580,24 +545,28 @@\n \n **Options**\n \n-- "automatic combination": files are automatically arranged in a grid (duplicated pixels are allowed), subfiles are named according to the input file name\n+- "automatic combination": files are automatically arranged in a grid, subfiles are named according to the input file name\n - "xy shifts": 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 as shown above). The xy shift option combines all datasets and removes all duplicated pixels (same x and y coordinates).\n+- "Set all file coordinates to 1/1 as origin" can be choosen to override current pixel coordinates of the input file and set their minimal x and minimal y values to 1. Then the shifts from the xy shift tabular files are used to move the pixels of each dataset. \n+- In case the input files have not exactly the same m/z values set "Do the files have different m/z axis?" to "Yes". Then functionalities of the "MALDIquant" package are used to combine the datasets. \n+\n \n **Tips**\n \n-- The combine tools puts all samples into a common x-y-grid, therefore pixel coordinates will change. In case the pixels are already annotated, the annotations should be provided as tabular files and the tool will return an annotation file with the new pixel coordinates. This annotation file can then be used together with the combined MSI data for tools in which the annotation is required (e.g. \'MSI classification\') or useful (e.g. \'MSI spectra plots\').\n-- In case more annotations are required: The annotation input file should have an identifier column, for example the patient_ID. A second tabular file that contains more annotations and also one column with the identifier column (e.g. \'patient_ID\') can be merged to the annotation output file of this tool with the tool \'join two files\' and then set the \'Column to use\' parameters for both files to the identifier column. \n-\n+- The combine tool puts all samples into a common x-y-grid, therefore pixel coordinates will change. In case the pixels are already annotated, the annotations should be provided as tabular files and the tool will return an annotation file with the new pixel coordinates. This annotation file can then be used together with the combined MSI data for tools in which the annotation is required (e.g. \'MSI classification\') or useful (e.g. \'MSI spectra plots\').\n \n \n **Output**\n \n-- MSI data as imzML file or .RData (can be read with the Cardinal package in R)\n-- pdf that shows the pixel positions and annotations of the combined files\n-- Tabular file with pixel annotations (x,y,column with input file names and up to five annotation columns)\n+- MSI data as imzML file (in continous format when m/z axis were the same; in processed format when m/z axis were different)\n+- Pdf with pixel positions and annotations of the combined files\n+- Tabular file with pixel annotations (x,y,column with input file names and annotation columns)\n \n \n ]]>\n </help>\n- <expand macro="citations"/>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btv146</citation>\n+ <citation type="doi">10.1007/978-3-319-45809-0_6</citation>\n+ </citations>\n </tool>\n' |
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| diff -r 48c07268f341 -r b41107d8fe89 test-data/112_annotation_output.tabular --- a/test-data/112_annotation_output.tabular Fri Mar 22 08:18:29 2019 -0400 +++ b/test-data/112_annotation_output.tabular Fri Dec 13 13:54:23 2019 -0500 |
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| @@ -1,16 +1,16 @@ -x y sample_name file_name column_name NA.x NA.y NA -1 1 msidata_1.RData file_one col1 NA NA NA -1 2 msidata_1.RData file_one col1 NA NA NA -1 3 msidata_1.RData file_one col1 NA NA NA -10 1 123_combined.RData file_two col3 NA NA NA -10 2 123_combined.RData file_two col3 NA NA NA -10 3 123_combined.RData file_two col3 NA NA NA -15 1 123_combined.RData file_three col3 NA NA NA -15 2 123_combined.RData file_three col3 NA NA NA -15 3 123_combined.RData file_three col3 NA NA NA -7 1 123_combined.RData file_one col1 NA NA NA -7 2 123_combined.RData file_one col1 NA NA NA -7 3 123_combined.RData file_one col1 NA NA NA -9 1 123_combined.RData file_two col2 NA NA NA -9 2 123_combined.RData file_two col2 NA NA NA -9 3 123_combined.RData file_two col2 NA NA NA +x y sample_name file_name column_name +1 1 msidata_1.RData file_one col1 +1 2 msidata_1.RData file_one col1 +1 3 msidata_1.RData file_one col1 +7 1 123_combined.RData file_one col1 +7 2 123_combined.RData file_one col1 +7 3 123_combined.RData file_one col1 +9 1 123_combined.RData file_two col2 +10 1 123_combined.RData file_two col3 +9 2 123_combined.RData file_two col2 +10 2 123_combined.RData file_two col3 +9 3 123_combined.RData file_two col2 +10 3 123_combined.RData file_two col3 +15 1 123_combined.RData file_three col3 +15 2 123_combined.RData file_three col3 +15 3 123_combined.RData file_three col3 |
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| diff -r 48c07268f341 -r b41107d8fe89 test-data/112_auto_combined.ibd |
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| Binary file test-data/112_auto_combined.ibd has changed |
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| diff -r 48c07268f341 -r b41107d8fe89 test-data/112_auto_combined.imzml --- a/test-data/112_auto_combined.imzml Fri Mar 22 08:18:29 2019 -0400 +++ b/test-data/112_auto_combined.imzml Fri Dec 13 13:54:23 2019 -0500 |
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| @@ -9,8 +9,8 @@ <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" /> <cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{00A83E55-A8F8-41D4-BBAC-345FA77AAB7E}" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9B17E43E3D3B35BE3CD0AE65F40E0C6B27C2752F" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="a0620366-fee2-4a2a-a643-0f0e0c9ae5a6" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9bcd78ace1e6441dc527501b5eb3994fcf15b894" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -22,19 +22,18 @@ </referenceableParamGroup> <referenceableParamGroup id="scan1"> <cvParam cvRef="MS" accession="MS:1000093" name="increasing m/z scan" value="" /> - <cvParam cvRef="MS" accession="MS:1000095" name="linear" value="" /> </referenceableParamGroup> <referenceableParamGroup id="mzArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000514" name="m/z array" value="" unitCvRef="MS" unitAccession="MS:1000040" unitName="m/z" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> <referenceableParamGroup id="intensityArray"> <cvParam cvRef="MS" accession="MS:1000576" name="no compression" value="" /> <cvParam cvRef="MS" accession="MS:1000515" name="intensity array" value="" unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts" /> <cvParam cvRef="IMS" accession="IMS:1000101" name="external data" value="true" /> - <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="32-bit float" /> + <cvParam cvRef="MS" accession="MS:1000521" name="32-bit float" value="" /> </referenceableParamGroup> </referenceableParamGroupList> <sampleList count="1"> @@ -43,18 +42,24 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="1.12.1"> + <software id="Cardinal" version="2.2.6"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> <scanSettingsList count="1"> <scanSettings id="scansettings1"> - <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="15" /> + <cvParam cvRef="IMS" accession="IMS:1000042" name="max count of pixel x" value="5" /> <cvParam cvRef="IMS" accession="IMS:1000043" name="max count of pixel y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000044" name="max dimension x" value="15" /> + <cvParam cvRef="IMS" accession="IMS:1000045" name="max dimension y" value="3" /> + <cvParam cvRef="IMS" accession="IMS:1000046" name="pixel size x" value="1.000000" /> + <cvParam cvRef="IMS" accession="IMS:1000047" name="pixel size y" value="1.000000" /> </scanSettings> </scanSettingsList> <instrumentConfigurationList count="1"> - <instrumentConfiguration id="IC1" /> + <instrumentConfiguration id="IC1"> + <cvParam cvRef="MS" accession="MS:1000031" name="instrument model" /> + </instrumentConfiguration> </instrumentConfigurationList> <dataProcessingList count="1"> <dataProcessing id="CardinalWriteImzML"> |
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| diff -r 48c07268f341 -r b41107d8fe89 test-data/112_auto_combined.imzml.txt --- a/test-data/112_auto_combined.imzml.txt Fri Mar 22 08:18:29 2019 -0400 +++ b/test-data/112_auto_combined.imzml.txt Fri Dec 13 13:54:23 2019 -0500 |
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| @@ -1,4 +1,4 @@ imzML file: total 556 --rw-r--r-- 1 meli meli 537552 Feb 12 12:25 ibd --rw-r--r-- 1 meli meli 25466 Feb 12 12:25 imzml +-rw-r--r-- 1 meli meli 537552 Dez 11 00:10 ibd +-rw-r--r-- 1 meli meli 25811 Dez 11 00:10 imzml |
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| diff -r 48c07268f341 -r b41107d8fe89 test-data/112_auto_combined_QC.pdf |
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| diff -r 48c07268f341 -r b41107d8fe89 test-data/123_annotation_output.tabular --- a/test-data/123_annotation_output.tabular Fri Mar 22 08:18:29 2019 -0400 +++ b/test-data/123_annotation_output.tabular Fri Dec 13 13:54:23 2019 -0500 |
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| @@ -1,13 +1,13 @@ -x y sample_name file_name column_name NA.x NA.y NA -1 1 File1 file_one col1 NA NA NA -1 2 File1 file_one col1 NA NA NA -1 3 File1 file_one col1 NA NA NA -3 1 File2 file_two col2 NA NA NA -3 2 File2 file_two col2 NA NA NA -3 3 File2 file_two col2 NA NA NA -4 1 File2 file_two col3 NA NA NA -4 2 File2 file_two col3 NA NA NA -4 3 File2 file_two col3 NA NA NA -9 1 File3 file_three col3 NA NA NA -9 2 File3 file_three col3 NA NA NA -9 3 File3 file_three col3 NA NA NA +x y sample_name file_name column_name +1 1 File1 file_one col1 +1 2 File1 file_one col1 +1 3 File1 file_one col1 +3 1 File2 file_two col2 +4 1 File2 file_two col3 +3 2 File2 file_two col2 +4 2 File2 file_two col3 +3 3 File2 file_two col2 +4 3 File2 file_two col3 +9 1 File3 file_three col3 +9 2 File3 file_three col3 +9 3 File3 file_three col3 |
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| diff -r 48c07268f341 -r b41107d8fe89 test-data/123_combined.ibd |
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| diff -r 48c07268f341 -r b41107d8fe89 test-data/123_combined.imzml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/123_combined.imzml Fri Dec 13 13:54:23 2019 -0500 |
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| b'@@ -0,0 +1,399 @@\n+<?xml version="1.0"?>\n+<mzML version="1.1" 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">\n+\t<cvList count="3">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" version="1.3.1" URI="http://psidev.info/ms/mzML/psi-ms.obo" />\n+\t\t<cv id="UO" fullName="Unit Ontology" version="1.15" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />\n+\t\t<cv id="IMS" fullName="Imaging MS Ontology" version="0.9.1" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" />\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum" value="" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally 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