| Next changeset 1:0892a051eb17 (2018-10-01) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/MALDIquant commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6 |
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added:
maldi_macros.xml maldi_quant_preprocessing.xml test-data/Analyze75.hdr test-data/Analyze75.img test-data/Analyze75.t2m test-data/Example_Continuous.ibd test-data/Example_Continuous.imzML test-data/Preprocessing1_QC.pdf test-data/Preprocessing2_QC.pdf test-data/Preprocessing3_QC.pdf test-data/align_reference_test2.tabular test-data/annotations_output3.tabular test-data/int1.tabular test-data/int2.tabular test-data/intensity_matrix3.tabular test-data/masspeaks1.tabular test-data/masspeaks1_forinput.tabular test-data/masspeaks2.tabular test-data/masspeaks3.tabular test-data/msidata_1.RData test-data/outfile1.ibd test-data/outfile1.imzML test-data/outfile2.ibd test-data/outfile2.imzML test-data/outfile3.ibd test-data/outfile3.imzML test-data/peakdetection1_QC.pdf test-data/peakdetection2_QC.pdf test-data/peakdetection3_QC.pdf test-data/pixel_annotations.tabular test-data/restricted_pixels.tabular |
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| diff -r 000000000000 -r e2aa05746a69 maldi_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maldi_macros.xml Wed Aug 22 11:49:06 2018 -0400 |
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| @@ -0,0 +1,26 @@ +<macros> + <token name="@R_IMPORTS@"><![CDATA[ + ## Libraries + library (Cardinal) + library (MALDIquantForeign) + library (MALDIquant) + library (ggplot2) + + ]]> + </token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement> + <requirement type="package" version="0.11.5">r-maldiquantforeign</requirement> + <requirement type="package" version="1.18">r-maldiquant</requirement> + <requirement type="package" version="2.2.1">r-ggplot2</requirement> + </requirements> + </xml> + + <xml name="citation"> + <citations> + <citation type="doi">10.1093/bioinformatics/bts447</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r e2aa05746a69 maldi_quant_preprocessing.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maldi_quant_preprocessing.xml Wed Aug 22 11:49:06 2018 -0400 |
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| b'@@ -0,0 +1,509 @@\n+<tool id="maldi_quant_preprocessing" name="MALDIquant preprocessing" version="1.18.0.0">\r\n+ <description>\r\n+ Preprocessing of mass-spectrometry imaging data\r\n+ </description>\r\n+ <macros>\r\n+ <import>maldi_macros.xml</import>\r\n+ </macros>\r\n+ <expand macro="requirements"/>\r\n+ <command detect_errors="exit_code">\r\n+ <![CDATA[\r\n+ #if $infile.ext == \'imzml\'\r\n+ cp \'${infile.extra_files_path}/imzml\' infile.imzML &&\r\n+ cp \'${infile.extra_files_path}/ibd\' infile.ibd &&\r\n+ #elif $infile.ext == \'analyze75\'\r\n+ cp \'${infile.extra_files_path}/hdr\' infile.hdr &&\r\n+ cp \'${infile.extra_files_path}/img\' infile.img &&\r\n+ cp \'${infile.extra_files_path}/t2m\' infile.t2m &&\r\n+ du infile.hdr &&\r\n+ du infile.img &&\r\n+ du -s -B1 infile.hdr &&\r\n+ #else\r\n+ ln -s $infile infile.RData &&\r\n+ #end if\r\n+ Rscript "${maldi_quant_preprocessing}" &&\r\n+ mkdir $outfile_imzml.files_path &&\r\n+ mv ./out.imzMl "${os.path.join($outfile_imzml.files_path, \'imzml\')}" | true &&\r\n+ mv ./out.ibd "${os.path.join($outfile_imzml.files_path, \'ibd\')}" | true &&\r\n+ echo "imzML file:" > $outfile_imzml &&\r\n+ ls -l "$outfile_imzml.files_path" >> $outfile_imzml\r\n+ ]]>\r\n+ </command>\r\n+ <configfiles>\r\n+ <configfile name="maldi_quant_preprocessing"><![CDATA[\r\n+\r\n+@R_IMPORTS@\r\n+\r\n+#if $restriction_conditional.restriction == \'restrict\':\r\n+\r\n+ print(\'Reading mask region\')\r\n+ ## Import imzML file\r\n+\r\n+ coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = FALSE, stringsAsFactors = FALSE))[,1:2]\r\n+\r\n+ maldi_data = importImzMl(\'infile.imzML\',\r\n+ coordinates = coordinate_matrix)\r\n+ pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])\r\n+\r\n+#else:\r\n+\r\n+ print(\'Reading entire file\')\r\n+ #if $infile.ext == \'imzml\'\r\n+ ## Import imzML file\r\n+ maldi_data = import( \'infile.imzML\', type="imzML" )\r\n+ #elif $infile.ext == \'analyze75\'\r\n+ ## Import analyze7.5 file\r\n+ maldi_data = import( \'infile.hdr\' )\r\n+ #else\r\n+ loadRData <- function(fileName){\r\n+ #loads an RData file, and returns it\r\n+ load(fileName)\r\n+ get(ls()[ls() != "fileName"])\r\n+ }\r\n+ msidata = loadRData(\'infile.RData\')\r\n+\r\n+ ## save coordinates\r\n+ cardinal_coordinates = as.matrix(Cardinal::coord(msidata)[,1:2])\r\n+ ## save mz values\r\n+ cardinal_mzs = Cardinal::mz(msidata)\r\n+ ## create MALDIquant MassSpectrum object\r\n+ maldi_data = list()\r\n+ for(number_spectra in 1:ncol(msidata)){\r\n+ maldi_data[[number_spectra]] = createMassSpectrum(mass = cardinal_mzs, intensity = iData(msidata)[,number_spectra])\r\n+ }\r\n+\r\n+ #end if\r\n+\r\n+#end if\r\n+\r\n+## Quality control plots during preprocessing \r\n+\r\n+pdf("prepro_qc_plot.pdf", fonts = "Times", pointsize = 12)\r\n+plot(0,type=\'n\',axes=FALSE,ann=FALSE)\r\n+\r\n+## if no filename is given, name of file in Galaxy history is used\r\n+ #set $filename = $infile.display_name\r\n+title(main=paste("$filename"))\r\n+\r\n+#if str($tabular_annotation.load_annotation) == \'yes_annotation\':\r\n+ print("use annotation file")\r\n+ ## read and extract x,y,annotation information\r\n+ input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)\r\n+ annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]\r\n+ colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"\r\n+\r\n+ ## merge with coordinate information of MSI data\r\n+ coordinates_st = cbind(coordinates(maldi_data)[,1:2], c(1:length(maldi_data)))\r\n+ colnames(coordinates_st)[3] = "pixel'..b'/>\r\n+ <output name="outfile_imzml" file="outfile1.ibd" compare="sim_size"/>\r\n+ <output name="plots" file="Preprocessing1_QC.pdf" compare="sim_size"/>\r\n+ </test>\r\n+ <test>\r\n+ <param name="infile" value="msidata_1.RData" ftype="rdata"/>\r\n+ <conditional name="methods_conditional">\r\n+ <param name="method" value="Calibrate"/>\r\n+ <param name="calibrate_method" value="PQN"/>\r\n+ </conditional>\r\n+ <output name="outfile_imzml" file="outfile2.imzML" compare="sim_size"/>\r\n+ <output name="outfile_imzml" file="outfile2.ibd" compare="sim_size"/>\r\n+ <output name="plots" file="Preprocessing2_QC.pdf" compare="sim_size"/>\r\n+ </test>\r\n+ <test>\r\n+ <param name="infile" value="" ftype="imzml">\r\n+ <composite_data value="Example_Continuous.imzML"/>\r\n+ <composite_data value="Example_Continuous.ibd"/>\r\n+ </param>\r\n+ <conditional name="tabular_annotation">\r\n+ <param name="load_annotation" value="yes_annotation"/>\r\n+ <param name="annotation_file" value="pixel_annotations.tabular"/>\r\n+ <param name="column_x" value="1"/>\r\n+ <param name="column_y" value="2"/>\r\n+ <param name="column_names" value="3"/>\r\n+ <param name="tabular_header" value="TRUE"/>\r\n+ </conditional>\r\n+ <conditional name="methods_conditional">\r\n+ <param name="method" value="Align"/>\r\n+ <param name="warping_method" value="linear"/>\r\n+ <param name="halfWindowSize" value="1"/>\r\n+ <conditional name="reference_for_alignment">\r\n+ <param name="align_ref" value="yes_reference"/>\r\n+ <param name="reference_file" value="align_reference_test2.tabular" ftype="tabular"/>\r\n+ <param name="allow_nomatch" value="TRUE"/>\r\n+ <param name="remove_empty" value="TRUE"/>\r\n+ <param name="empty_nomatch" value="TRUE"/>\r\n+ </conditional>\r\n+ </conditional>\r\n+ <output name="outfile_imzml" file="outfile3.imzML" compare="sim_size"/>\r\n+ <output name="outfile_imzml" file="outfile3.ibd" compare="sim_size"/>\r\n+ <output name="plots" file="Preprocessing3_QC.pdf" compare="sim_size"/>\r\n+ <output name="annotation_output" file="annotations_output3.tabular"/>\r\n+ </test>\r\n+ </tests>\r\n+ <help><![CDATA[\r\n+\r\n+MALDIquant_ provides a complete analysis pipeline for MALDI-TOF and other mass spectrometry data. So far we have only implemented the functionalities for mass spectrometry imaging data.\r\n+\r\n+Input data: \r\n+\r\n+- MSI data as imzML file (upload via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_\r\n+- optinal tabular file with pixel coordinates to restrict reading of imzML file to coordinates of interest\r\n+\r\n+Options:\r\n+\r\n+- Transformation: transformation of intensities with log, log2, log10 and squareroot\r\n+- Smoothing: Smoothing of the peaks reduces noise and improves peak detection. Available smoothing methods are SavitzkyGolay and Moving Average\r\n+- Baseline reduction: Baseline reduction removes background intensity generated by chemical noise (common in MALDI datasets). Available methods are SNIP, TopHat,ConvexHull and median.\r\n+- Intensity calibration (normalization): Normalization of intensities to Total Ion Current (TIC), median spectrum, Probabilistic Quotient Normalization (PQN)\r\n+- Spectra alignment (warping):alignment for (re)calibration of m/z values\r\n+\r\n+\r\n+Output: \r\n+\r\n+- imzML file (imzML format can be continuous or processed)\r\n+- pdf with average mass spectra after each preprocessing step\r\n+\r\n+.. _MALDIquant: http://strimmerlab.org/software/maldiquant/\r\n+\r\n+ ]]>\r\n+ </help>\r\n+ <expand macro="citation"/>\r\n+</tool>\r\n' |
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| diff -r 000000000000 -r e2aa05746a69 test-data/Example_Continuous.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Example_Continuous.imzML Wed Aug 22 11:49:06 2018 -0400 |
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| diff -r 000000000000 -r e2aa05746a69 test-data/int1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int1.tabular Wed Aug 22 11:49:06 2018 -0400 |
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| @@ -0,0 +1,91 @@ +mz | spectra col1 col2 col3 +300.083343505859 0 0.0878976186116536 0 +304 9.438736829163e-11 0.137228806813558 0.203098436196645 +304.166687011719 0.104457606871923 0.0169352528949116 0.00765286510187286 +304.666687011719 0.00242311644190166 0.15201666439801 0.269343495368958 +305 0.238949338595072 0 0 +305.75 6.17044061804064e-07 0.155222187439613 1.2719295986822e-09 +305.916687011719 4.33073489900975e-15 0.20923868753016 0.186377684291186 +306.25 0.133792817751516 3.32863570899159e-06 0.00443744411071142 +306.666687011719 0.232789536317284 4.21300777966646e-07 0.00672620768781245 +306.916687011719 0.322907487551371 0.0935481031580518 0.012873843312233 +307.083343505859 0.146026631196443 0.151374835480731 0.218145370482365 +307.166687011719 0.0322767967978232 0.0595835944471799 0.48292171999357 +307.75 4.47047947697381e-07 0.14276859164238 2.35246092014329e-05 +308 4.74193198607586e-31 0.0105287345747153 0.107646773258845 +308.25 1.31886150149067e-10 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0.264233609040578 +393.583343505859 0 0.136588126420975 8.05443629544114e-18 +394.833343505859 0 6.62304192985937e-11 0.103502949078878 +395.916687011719 0.170605540275574 2.68065472318023e-19 4.58339070400444e-10 +397.083343505859 0.0962067842483521 5.10727327656766e-39 1.3634908830594e-18 +398.166687011719 4.69207117603236e-10 0 0.142847468455633 +398.75 0.214157521724701 0 0.0781838993231456 |
| b |
| diff -r 000000000000 -r e2aa05746a69 test-data/intensity_matrix3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/intensity_matrix3.tabular Wed Aug 22 11:49:06 2018 -0400 |
| b |
| b'@@ -0,0 +1,61 @@\n+mz | spectra\tx = 1, y = 1\tx = 2, y = 1\tx = 3, y = 1\tx = 1, y = 2\tx = 2, y = 2\tx = 3, y = 2\tx = 1, y = 3\tx = 2, y = 3\tx = 3, y = 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|
| b |
| diff -r 000000000000 -r e2aa05746a69 test-data/masspeaks1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masspeaks1.tabular Wed Aug 22 11:49:06 2018 -0400 |
| b |
| @@ -0,0 +1,99 @@ +snr mass intensity spectrum +5.34196717869329 304.166687011719 0.104457606871923 col1 +12.0922480027988 305 0.238949338595072 col1 +6.80380283473404 306.25 0.133792817751516 col1 +11.9239943102966 306.666687011719 0.232789536317284 col1 +16.7672721943661 306.916687011719 0.322907487551371 col1 +14.5727405573344 315.916687011719 0.134740673005581 col1 +12.6587975530526 316.25 0.117780188719432 col1 +15.5891513371263 320.916687011719 0.0873032609621684 col1 +8.28066653191209 322.75 0.107258200645447 col1 +8.64305080588796 327.083343505859 0.593451981743177 col1 +22.5976205263238 329 1.80600585540136 col1 +6.62986417925206 343.083343505859 0.319934318463008 col1 +5.76872573536526 343.75 0.314895849686906 col1 +7.23012875909998 344 0.41009783744812 col1 +12.5923211364761 345 0.777459700902303 col1 +5.61154187261139 346.083343505859 0.311080597071943 col1 +11.6128628366043 353.083343505859 0.0853602389494578 col1 +8.93926402677033 355.166687011719 0.093819797039032 col1 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367.916687011719 0.225095887978872 col2 +14.4139559364593 369.083343505859 0.167913814385732 col2 +13.4612234580055 370.416687011719 0.129989445209503 col2 +10.0270809962262 376 0.0839582482973735 col2 +13.7957864133576 378.75 0.090022732814153 col2 +21.7167106106545 382.583343505859 0.111637224753698 col2 +37.803872450968 383.166687011719 0.194509585698446 col2 +19.3443105357995 386.75 0.0984363655249278 col2 +40.2946953152003 393.583343505859 0.136588126420975 col2 +10.9042784289401 304 0.203098436196645 col3 +14.2536155186416 304.666687011719 0.269343495368958 col3 +9.73428286587393 305.916687011719 0.186377684291186 col3 +25.326392266369 307.166687011719 0.48292171999357 col3 +5.77081370276002 308 0.107646773258845 col3 +9.71607704287468 309.833343505859 0.161644687255224 col3 +12.3286648153297 314.75 0.168087442715963 col3 +10.0188114825306 314.916687011719 0.136831253767014 col3 +9.98544088935621 318.083343505859 0.131532917420069 col3 +15.9567928309838 318.416687011719 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+9.49389038421466 387.5 0.135613699754079 col3 +6.40597511255643 390.166687011719 0.0942935446898143 col3 +6.91093965563744 391.083343505859 0.103488087654114 col3 +12.1864531063779 392 0.184977193673452 col3 +17.1091639921622 392.833343505859 0.264233609040578 col3 +6.41767571506743 394.833343505859 0.103502949078878 col3 +8.23619853479686 398.166687011719 0.142847468455633 col3 |
| b |
| diff -r 000000000000 -r e2aa05746a69 test-data/masspeaks1_forinput.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masspeaks1_forinput.tabular Wed Aug 22 11:49:06 2018 -0400 |
| b |
| @@ -0,0 +1,99 @@ +snr mass intensity spectrum +5.34196717869329 304.166687011719 0.104457606871923 x = 1, y = 1 +12.0922480027988 305 0.238949338595072 x = 1, y = 1 +6.80380283473404 306.25 0.133792817751516 x = 1, y = 1 +11.9239943102966 306.666687011719 0.232789536317284 x = 1, y = 1 +16.7672721943661 306.916687011719 0.322907487551371 x = 1, y = 1 +14.5727405573344 315.916687011719 0.134740673005581 x = 1, y = 1 +12.6587975530526 316.25 0.117780188719432 x = 1, y = 1 +15.5891513371263 320.916687011719 0.0873032609621684 x = 1, y = 1 +8.28066653191209 322.75 0.107258200645447 x = 1, y = 1 +8.64305080588796 327.083343505859 0.593451981743177 x = 1, y = 1 +22.5976205263238 329 1.80600585540136 x = 1, y = 1 +6.62986417925206 343.083343505859 0.319934318463008 x = 1, y = 1 +5.76872573536526 343.75 0.314895849686906 x = 1, y = 1 +7.23012875909998 344 0.41009783744812 x = 1, y = 1 +12.5923211364761 345 0.777459700902303 x = 1, y = 1 +5.61154187261139 346.083343505859 0.311080597071943 x = 1, y = 1 +11.6128628366043 353.083343505859 0.0853602389494578 x = 1, y = 1 +8.93926402677033 355.166687011719 0.093819797039032 x = 1, y = 1 +11.4518402499656 355.916687011719 0.124494592348735 x = 1, y = 1 +12.2687590055812 356.916687011719 0.131409923235575 x = 1, y = 1 +17.1598526473503 360.916687011719 0.159461249907811 x = 1, y = 1 +19.5606964350667 364.333343505859 0.279228508472443 x = 1, y = 1 +13.4363791597757 365.583343505859 0.189359684795294 x = 1, y = 1 +7.2659142337533 366.083343505859 0.0986319063122271 x = 1, y = 1 +6.78882554537553 367.583343505859 0.0783568720022837 x = 1, y = 1 +19.2913990161673 370.083343505859 0.149130453666051 x = 1, y = 1 +22.9258781818056 374.5 0.10046042005221 x = 1, y = 1 +32.553974512381 395.916687011719 0.170605540275574 x = 1, y = 1 +20.0044568991975 397.083343505859 0.0962067842483521 x = 1, y = 1 +52.5251008144488 398.75 0.214157521724701 x = 1, y = 1 +6.53932310180994 300.083343505859 0.0878976186116536 x = 2, y = 1 +8.1332053348611 304 0.137228806813558 x = 2, y = 1 +8.87376047659255 304.666687011719 0.15201666439801 x = 2, y = 1 +9.0031548908286 305.75 0.155222187439613 x = 2, y = 1 +12.1483037475036 305.916687011719 0.20923868753016 x = 2, y = 1 +5.50393277232579 306.916687011719 0.0935481031580518 x = 2, y = 1 +8.92694410124806 307.083343505859 0.151374835480731 x = 2, y = 1 +8.53366295883023 307.75 0.14276859164238 x = 2, y = 1 +20.8363523568967 308.25 0.34317347407341 x = 2, y = 1 +9.03952553159105 311.5 0.126103460788727 x = 2, y = 1 +9.21792692425819 313.166687011719 0.11177615324661 x = 2, y = 1 +10.2836388640006 314 0.114434331655502 x = 2, y = 1 +14.5366950159814 315.833343505859 0.110506186882656 x = 2, y = 1 +29.6030745455647 321.25 0.0977287689844767 x = 2, y = 1 +5.12133326721085 327.916687011719 0.406224122348552 x = 2, y = 1 +18.2260181460723 328.916687011719 1.60846790671349 x = 2, y = 1 +6.71691695849357 339.416687011719 0.214046796162923 x = 2, y = 1 +5.42044735697872 343.916687011719 0.369042471672098 x = 2, y = 1 +9.90109899068147 344.916687011719 0.751941124598185 x = 2, y = 1 +5.7761050136785 346 0.407967170079549 x = 2, y = 1 +9.53380778579935 350.083343505859 0.103204836448034 x = 2, y = 1 +22.3739163562105 357.333343505859 0.132146000862122 x = 2, y = 1 +17.1123310736305 359.916687011719 0.0798314611117045 x = 2, y = 1 +21.5296474065392 365.833343505859 0.247531970342 x = 2, y = 1 +17.6598326813686 367.916687011719 0.225095887978872 x = 2, y = 1 +14.4139559364593 369.083343505859 0.167913814385732 x = 2, y = 1 +13.4612234580055 370.416687011719 0.129989445209503 x = 2, y = 1 +10.0270809962262 376 0.0839582482973735 x = 2, y = 1 +13.7957864133576 378.75 0.090022732814153 x = 2, y = 1 +21.7167106106545 382.583343505859 0.111637224753698 x = 2, y = 1 +37.803872450968 383.166687011719 0.194509585698446 x = 2, y = 1 +19.3443105357995 386.75 0.0984363655249278 x = 2, y = 1 +40.2946953152003 393.583343505859 0.136588126420975 x = 2, y = 1 +10.9042784289401 304 0.203098436196645 x = 3, y = 1 +14.2536155186416 304.666687011719 0.269343495368958 x = 3, y = 1 +9.73428286587393 305.916687011719 0.186377684291186 x = 3, y = 1 +25.326392266369 307.166687011719 0.48292171999357 x = 3, y = 1 +5.77081370276002 308 0.107646773258845 x = 3, y = 1 +9.71607704287468 309.833343505859 0.161644687255224 x = 3, y = 1 +12.3286648153297 314.75 0.168087442715963 x = 3, y = 1 +10.0188114825306 314.916687011719 0.136831253767014 x = 3, y = 1 +9.98544088935621 318.083343505859 0.131532917420069 x = 3, y = 1 +15.9567928309838 318.416687011719 0.202652255694071 x = 3, y = 1 +5.45721434599321 326.916687011719 0.25384642680486 x = 3, y = 1 +6.94450239587698 328 0.340036729971568 x = 3, y = 1 +26.3506501037786 328.916687011719 1.28705859184265 x = 3, y = 1 +21.9755116973922 329.083343505859 1.05529999732971 x = 3, y = 1 +6.26698769334215 342.333343505859 0.19008461634318 x = 3, y = 1 +7.40453698942461 343.916687011719 0.2857492963473 x = 3, y = 1 +5.47629632143471 344.333343505859 0.225824773311615 x = 3, y = 1 +24.2489760518392 345.083343505859 1.09834182262421 x = 3, y = 1 +7.55360848799134 346 0.326915502548218 x = 3, y = 1 +31.8141872712877 355.333343505859 0.218277891476949 x = 3, y = 1 +28.500421447754 359.916687011719 0.0977983176708221 x = 3, y = 1 +35.9263674883478 370.333343505859 0.318489452203115 x = 3, y = 1 +17.9023349585808 376.833343505859 0.119955976804097 x = 3, y = 1 +14.165837350632 379.5 0.138252675533295 x = 3, y = 1 +6.1026956808649 380.75 0.063951442639033 x = 3, y = 1 +6.66805606030542 386.666687011719 0.0939600268999736 x = 3, y = 1 +10.4761700777795 387 0.148616979519526 x = 3, y = 1 +14.9996173987781 387.166687011719 0.213376681009928 x = 3, y = 1 +9.49389038421466 387.5 0.135613699754079 x = 3, y = 1 +6.40597511255643 390.166687011719 0.0942935446898143 x = 3, y = 1 +6.91093965563744 391.083343505859 0.103488087654114 x = 3, y = 1 +12.1864531063779 392 0.184977193673452 x = 3, y = 1 +17.1091639921622 392.833343505859 0.264233609040578 x = 3, y = 1 +6.41767571506743 394.833343505859 0.103502949078878 x = 3, y = 1 +8.23619853479686 398.166687011719 0.142847468455633 x = 3, y = 1 |
| b |
| diff -r 000000000000 -r e2aa05746a69 test-data/masspeaks3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masspeaks3.tabular Wed Aug 22 11:49:06 2018 -0400 |
| b |
| b'@@ -0,0 +1,298 @@\n+snr\tmass\tintensity\tspectrum\n+Inf\t304.595254080636\t1.76512676262064e-05\tx = 1, y = 1\n+Inf\t305.119057791574\t1.62699820283052e-09\tx = 1, y = 1\n+Inf\t305.66667175293\t1.02237303638199e-13\tx = 1, y = 1\n+Inf\t306.32292175293\t7.71168242810122e-18\tx = 1, y = 1\n+Inf\t307.031265258789\t5.54882387838857e-22\tx = 1, y = 1\n+Inf\t307.614593505859\t3.61475171997316e-26\tx = 1, y = 1\n+Inf\t308.718757629395\t1.67789168240286e-34\tx = 1, y = 1\n+Inf\t309.250011444092\t1.43981749664202e-38\tx = 1, y = 1\n+Inf\t321.050012207031\t1.5556590571819e-38\tx = 1, y = 1\n+Inf\t328.000010172526\t0.481155782938004\tx = 1, y = 1\n+Inf\t329.152786254883\t2.47849035263062\tx = 1, y = 1\n+Inf\t330.197929382324\t1.09462394703996e-08\tx = 1, y = 1\n+Inf\t330.712968614366\t5.96421675068404e-13\tx = 1, y = 1\n+Inf\t331.259270562066\t5.44180783738833e-17\tx = 1, y = 1\n+Inf\t331.796308729384\t2.72964412068832e-21\tx = 1, y = 1\n+Inf\t332.342600504557\t2.65403450832136e-25\tx = 1, y = 1\n+Inf\t332.879638671875\t1.38079261482617e-29\tx = 1, y = 1\n+Inf\t333.44445461697\t1.27447841383671e-33\tx = 1, y = 1\n+Inf\t343.642865862165\t0.282461315393448\tx = 1, y = 1\n+Inf\t344.611124674479\t0.638258039951324\tx = 1, y = 1\n+Inf\t345.629638671875\t7.93658109614626e-05\tx = 1, y = 1\n+Inf\t346.120378282335\t6.64322641341641e-09\tx = 1, y = 1\n+Inf\t346.700012207031\t3.66650991252132e-13\tx = 1, y = 1\n+Inf\t347.296308729384\t3.31281302377731e-17\tx = 1, y = 1\n+Inf\t347.814826117622\t1.67992344863529e-21\tx = 1, y = 1\n+Inf\t348.361117892795\t1.61966283306326e-25\tx = 1, y = 1\n+Inf\t348.888895670573\t8.15391718679523e-30\tx = 1, y = 1\n+Inf\t349.44445461697\t7.79337969080295e-34\tx = 1, y = 1\n+Inf\t349.96297539605\t4.78329195057699e-38\tx = 1, y = 1\n+Inf\t365.979179382324\t3.88570062627783e-13\tx = 1, y = 1\n+Inf\t366.562515258789\t1.91497258346089e-17\tx = 1, y = 1\n+Inf\t367.083343505859\t1.88767583715038e-21\tx = 1, y = 1\n+Inf\t367.645835876465\t0.235070616006851\tx = 1, y = 1\n+Inf\t368.222229003906\t1.47346945595928e-05\tx = 1, y = 1\n+Inf\t368.666680908203\t1.13727949280218e-09\tx = 1, y = 1\n+Inf\t369.216674804688\t6.86236075017783e-14\tx = 1, y = 1\n+Inf\t369.766680908203\t5.79879376075753e-18\tx = 1, y = 1\n+Inf\t370.523821149554\t2.65765684162034e-05\tx = 1, y = 1\n+Inf\t306.32292175293\t1.93815667444142e-05\tx = 2, y = 1\n+Inf\t307.031265258789\t1.36712752230039e-09\tx = 2, y = 1\n+Inf\t307.614593505859\t9.10052605105835e-14\tx = 2, y = 1\n+Inf\t308.266668701172\t0.399492412805557\tx = 2, y = 1\n+Inf\t308.718757629395\t2.19716112042079e-05\tx = 2, y = 1\n+Inf\t309.250011444092\t1.93809390758304e-09\tx = 2, y = 1\n+Inf\t309.833347865513\t1.00940015081239e-13\tx = 2, y = 1\n+Inf\t310.361124674479\t9.53307623430011e-18\tx = 2, y = 1\n+Inf\t310.902786254883\t4.60080996999485e-22\tx = 2, y = 1\n+Inf\t311.430557250977\t0.37831038236618\tx = 2, y = 1\n+Inf\t311.986119588216\t3.04782115563285e-05\tx = 2, y = 1\n+Inf\t312.516674804688\t1.61912494522909e-09\tx = 2, y = 1\n+Inf\t328.937515258789\t2.02454543113708\tx = 2, y = 1\n+Inf\t329.697925567627\t4.36672562500462e-05\tx = 2, y = 1\n+Inf\t330.197929382324\t0.291347920894623\tx = 2, y = 1\n+Inf\t330.712968614366\t2.65860908257309e-05\tx = 2, y = 1\n+Inf\t331.259270562066\t1.33338984298348e-09\tx = 2, y = 1\n+Inf\t331.796308729384\t0.256167501211166\tx = 2, y = 1\n+Inf\t332.342600504557\t1.61519819812384e-05\tx = 2, y = 1\n+Inf\t332.879638671875\t0.473990738391876\tx = 2, y = 1\n+Inf\t333.44445461697\t3.11978510580957e-05\tx = 2, y = 1\n+Inf\t334.020843505859\t2.16568318833765e-09\tx = 2, y = 1\n+Inf\t343.642865862165\t4.07043262384832e-05\tx = 2, y = 1\n+Inf\t345.629638671875\t0.388675004243851\tx = 2, y = 1\n+Inf\t346.120378282335\t1.22390151023865\tx = 2, y = 1\n+Inf\t347.296308729384\t2.53151047218125e-05\tx = 2, y = 1\n+Inf\t347.814826117622\t2.07963690712631e-09\tx = 2, y = 1\n+Inf\t348.361117892795\t1.17175312421697e-13\tx = 2, y = 1\n+Inf\t348.888895670573\t1.04223425420895e-17\tx = 2, y = 1\n+Inf\t349.44445461697\t5.37785487481536e-22\tx = 2, y = 1\n+Inf\t349.96297539605\t0.309614509344101\tx = 2, y = 1\n+Inf\t351.069458007812\t1.2832610529756e-09\tx = 2, y = 1\n+Inf\t370.523821149554\t2.16230963798365e-13\tx = 2, y = 1\n+Inf\t328.937515258789\t1.431587338'..b'379808908e-30\tx = 1, y = 3\n+Inf\t349.44445461697\t2.58541051461361e-34\tx = 1, y = 3\n+Inf\t349.96297539605\t2.00786591889092e-38\tx = 1, y = 3\n+Inf\t365.979179382324\t0.29585200548172\tx = 1, y = 3\n+Inf\t366.562515258789\t2.61009136011126e-05\tx = 1, y = 3\n+Inf\t367.083343505859\t1.29202726295574e-09\tx = 1, y = 3\n+Inf\t367.645835876465\t1.26925610321495e-13\tx = 1, y = 3\n+Inf\t368.222229003906\t6.86202649112451e-18\tx = 1, y = 3\n+Inf\t368.666680908203\t6.0804923995715e-22\tx = 1, y = 3\n+Inf\t369.216674804688\t3.92168363149906e-26\tx = 1, y = 3\n+Inf\t369.766680908203\t2.87628364894794e-30\tx = 1, y = 3\n+Inf\t370.523821149554\t2.11079916033934e-34\tx = 1, y = 3\n+Inf\t306.32292175293\t2.58914169535274e-05\tx = 2, y = 3\n+Inf\t307.031265258789\t0.2786685526371\tx = 2, y = 3\n+Inf\t307.614593505859\t2.96689468086697e-05\tx = 2, y = 3\n+Inf\t308.266668701172\t0.630028009414673\tx = 2, y = 3\n+Inf\t308.718757629395\t3.5055691114394e-05\tx = 2, y = 3\n+Inf\t309.250011444092\t3.4764433554102e-09\tx = 2, y = 3\n+Inf\t309.833347865513\t2.08417769262566e-13\tx = 2, y = 3\n+Inf\t310.361124674479\t1.65365266219334e-17\tx = 2, y = 3\n+Inf\t310.902786254883\t1.14908291585848e-21\tx = 2, y = 3\n+Inf\t311.430557250977\t7.77481833182232e-26\tx = 2, y = 3\n+Inf\t311.986119588216\t6.04272858040201e-30\tx = 2, y = 3\n+Inf\t312.516674804688\t3.61853642833949e-34\tx = 2, y = 3\n+Inf\t328.937515258789\t1.3272477388382\tx = 2, y = 3\n+Inf\t329.697925567627\t0.000119319425721187\tx = 2, y = 3\n+Inf\t330.197929382324\t0.87813526391983\tx = 2, y = 3\n+Inf\t330.712968614366\t5.94691991864238e-05\tx = 2, y = 3\n+Inf\t331.259270562066\t4.48100578864796e-09\tx = 2, y = 3\n+Inf\t331.796308729384\t2.77607174444319e-13\tx = 2, y = 3\n+Inf\t332.342600504557\t2.30068624134988e-17\tx = 2, y = 3\n+Inf\t332.879638671875\t1.28379127790181e-21\tx = 2, y = 3\n+Inf\t333.44445461697\t1.15039499526719e-25\tx = 2, y = 3\n+Inf\t334.020843505859\t5.88708673366388e-30\tx = 2, y = 3\n+Inf\t343.642865862165\t0.628214061260223\tx = 2, y = 3\n+Inf\t345.629638671875\t2.52073332376312e-05\tx = 2, y = 3\n+Inf\t346.120378282335\t2.42913511527831e-09\tx = 2, y = 3\n+Inf\t347.296308729384\t3.06663314404432e-05\tx = 2, y = 3\n+Inf\t347.814826117622\t1.64383595624429e-09\tx = 2, y = 3\n+Inf\t348.361117892795\t1.4698648114625e-13\tx = 2, y = 3\n+Inf\t348.888895670573\t9.42402156952173e-18\tx = 2, y = 3\n+Inf\t349.44445461697\t6.95620575449764e-22\tx = 2, y = 3\n+Inf\t349.96297539605\t5.08223484114241e-26\tx = 2, y = 3\n+Inf\t351.069458007812\t2.63284561467787e-34\tx = 2, y = 3\n+Inf\t370.523821149554\t0.38996833562851\tx = 2, y = 3\n+Inf\t328.937515258789\t1.43404459953308\tx = 3, y = 3\n+Inf\t329.697925567627\t6.18351987213828e-05\tx = 3, y = 3\n+Inf\t330.712968614366\t3.4482751940304e-13\tx = 3, y = 3\n+Inf\t331.259270562066\t2.93395139921047e-17\tx = 3, y = 3\n+Inf\t331.796308729384\t1.94369975414076e-21\tx = 3, y = 3\n+Inf\t332.342600504557\t1.38486306848585e-25\tx = 3, y = 3\n+Inf\t332.879638671875\t1.03717248235199e-29\tx = 3, y = 3\n+Inf\t333.44445461697\t6.46787389371651e-34\tx = 3, y = 3\n+Inf\t334.020843505859\t5.33374608969737e-38\tx = 3, y = 3\n+Inf\t345.629638671875\t0.000100398268841673\tx = 3, y = 3\n+Inf\t346.120378282335\t0.700047612190247\tx = 3, y = 3\n+Inf\t347.296308729384\t0.290130436420441\tx = 3, y = 3\n+Inf\t347.814826117622\t1.69061459018849e-05\tx = 3, y = 3\n+Inf\t348.361117892795\t1.38276745609289e-09\tx = 3, y = 3\n+Inf\t348.888895670573\t9.4092654945744e-14\tx = 3, y = 3\n+Inf\t349.44445461697\t6.51254681822392e-18\tx = 3, y = 3\n+Inf\t349.96297539605\t4.97919259365601e-22\tx = 3, y = 3\n+Inf\t387.850006103516\t4.42154814663809e-05\tx = 3, y = 3\n+Inf\t388.895843505859\t2.20461995013854e-13\tx = 3, y = 3\n+Inf\t389.854179382324\t1.07776605300705e-21\tx = 3, y = 3\n+Inf\t391.083335876465\t5.18557991695755e-30\tx = 3, y = 3\n+Inf\t391.972229003906\t2.46211811583847e-38\tx = 3, y = 3\n+Inf\t394.083351135254\t0.225453585386276\tx = 3, y = 3\n+Inf\t394.791679382324\t0.310508847236633\tx = 3, y = 3\n+Inf\t395.270843505859\t2.11353399208747e-05\tx = 3, y = 3\n+Inf\t395.816680908203\t1.37501721120259e-09\tx = 3, y = 3\n+Inf\t396.383337402344\t9.99066823194339e-14\tx = 3, y = 3\n+Inf\t396.916674804687\t7.3794850397387e-18\tx = 3, y = 3\n' |
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| diff -r 000000000000 -r e2aa05746a69 test-data/outfile2.ibd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outfile2.ibd Wed Aug 22 11:49:06 2018 -0400 |
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| diff -r 000000000000 -r e2aa05746a69 test-data/outfile3.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outfile3.imzML Wed Aug 22 11:49:06 2018 -0400 |
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| @@ -0,0 +1,10 @@ +X Y annotation_name +1 1 col1 +1 2 col1 +1 3 col1 +2 1 col2 +2 2 col2 +2 3 col2 +3 1 col3 +3 2 col3 +3 3 col3 |
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