| Next changeset 1:eaaa73b043e6 (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_peakdetection.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 01212bf66f61 maldi_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maldi_macros.xml Wed Aug 22 11:49:29 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 01212bf66f61 maldi_quant_peakdetection.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maldi_quant_peakdetection.xml Wed Aug 22 11:49:29 2018 -0400 |
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| b'@@ -0,0 +1,505 @@\n+<tool id="maldi_quant_peak_detection" name="MALDIquant peak detection" version="1.18.0.0">\n+ <description>\n+ Peak detection, binning and filtering for mass-spectrometry imaging data\n+ </description>\n+ <macros>\n+ <import>maldi_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code">\n+ <![CDATA[\n+ #if $infile.ext == \'imzml\'\n+ cp \'${infile.extra_files_path}/imzml\' infile.imzML &&\n+ cp \'${infile.extra_files_path}/ibd\' infile.ibd &&\n+ #elif $infile.ext == \'analyze75\'\n+ cp \'${infile.extra_files_path}/hdr\' infile.hdr &&\n+ cp \'${infile.extra_files_path}/img\' infile.img &&\n+ cp \'${infile.extra_files_path}/t2m\' infile.t2m &&\n+ #end if\n+ Rscript \'${maldi_quant_peak_detection}\'&&\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+ </command>\n+ <configfiles>\n+ <configfile name="maldi_quant_peak_detection"><![CDATA[\n+\n+@R_IMPORTS@\n+\n+summarized_spectra = FALSE\n+\n+#if $restriction_conditional.restriction == \'restrict\':\n+\n+ print(\'Reading mask region\')\n+ ## Import imzML file\n+ coordinate_matrix = as.matrix(read.delim("$restriction_conditional.coordinates_file", header = FALSE, stringsAsFactors = FALSE))[,1:2]\n+\n+ maldi_data <- importImzMl(\'infile.imzML\',\n+ coordinates = coordinate_matrix, centroided = $centroids)\n+ pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])\n+\n+#else:\n+\n+ print(\'Reading entire file\')\n+ ## Import imzML file\n+\n+\n+ #if $infile.ext == \'imzml\'\n+\n+ #if str($centroids) == "TRUE"\n+ peaks <- importImzMl(\'infile.imzML\', centroided = $centroids)\n+ pixelnames = paste0("x = ", coordinates(peaks)[,1],", y = ", coordinates(peaks)[,2])\n+\n+ #else\n+ maldi_data <- importImzMl(\'infile.imzML\', centroided = $centroids)\n+ pixelnames = paste0("x = ", coordinates(maldi_data)[,1],", y = ", coordinates(maldi_data)[,2])\n+ #end if\n+ #elif $infile.ext == \'tabular\'\n+\n+ peak_tabular = read.delim("$infile", header = TRUE, stringsAsFactors = FALSE)\n+ peak_list = split(peak_tabular, f = peak_tabular\\$spectrum) ## will be ordered according to spectrum\n+ pixelnames = unique(peak_tabular\\$spectrum)\n+\n+ peaks = list()\n+ for (spectra in 1:length(peak_list))\n+ {\n+ single_peaks = createMassPeaks(peak_list[[spectra]]\\$mass, peak_list[[spectra]]\\$intensity, snr=peak_list[[spectra]]\\$snr)\n+ peaks[[spectra]] = single_peaks\n+ }\n+\n+ #end if\n+\n+\n+#end if\n+\n+## Quality control plots during peak detection\n+\n+pdf("peaks_qc_plot.pdf", fonts = "Times", pointsize = 12)\n+plot(0,type=\'n\',axes=FALSE,ann=FALSE)\n+\n+## if no filename is given, name of file in Galaxy history is used\n+#set $filename = $infile.display_name\n+\n+title(main=paste("$filename"))\n+\n+## plot input file spectrum: \n+#if $infile.ext == \'imzml\'\n+\n+ #if str($centroids) == "TRUE"\n+ plot(peaks[[1]], main="First spectrum of input file")\n+ #else\n+ avgSpectra <- averageMassSpectra(maldi_data,method="mean")\n+ plot(avgSpectra, main="Average spectrum of input file")\n+ #end if\n+#elif $infile.ext == \'tabular\'\n+ plot(peaks[[1]], main="First spectrum of input file")\n+#end if\n+\n+\n+#if str($tabular_annotation.load_annotation) == \'yes_annotation\':\n+\n+ ## read and extract x,y,annotation information\n+ input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)\n+ annotation_input = input_tabular[,c($tabular_annotation.'..b'="yes_annotation"/>\n+ <param name="annotation_file" value="pixel_annotations.tabular"/>\n+ <param name="column_x" value="1"/>\n+ <param name="column_y" value="2"/>\n+ <param name="column_names" value="3"/>\n+ <param name="tabular_header" value="TRUE"/>\n+ </conditional>\n+ <repeat name="methods">\n+ <conditional name="methods_conditional">\n+ <param name="method" value="Peak_detection"/>\n+ <param name="peak_method" value="MAD"/>\n+ <param name="halfWindowSize" value="1"/>\n+ <param name="snr" value="2"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="methods">\n+ <conditional name="methods_conditional">\n+ <param name="method" value="Binning"/>\n+ <param name="bin_tolerance" value="0.01"/>\n+ </conditional>\n+ </repeat>\n+ <repeat name="methods">\n+ <conditional name="methods_conditional">\n+ <param name="method" value="Filtering"/>\n+ <param name="bin_tolerance" value="0.01"/>\n+ <param name="minFrequency" value="0.5"/>\n+ <param name="minNumber" value="3"/>\n+ <param name="filter_annot_groups" value="TRUE"/>\n+ <param name="mergeWhitelists" value="FALSE"/>\n+ </conditional>\n+ </repeat>\n+ <output name="plots" file="peakdetection3_QC.pdf" compare="sim_size"/>\n+ <output name="intensity_matrix" file="intensity_matrix3.tabular"/>\n+ <output name="masspeaks" file="masspeaks3.tabular"/>\n+ </test>\n+ </tests>\n+ <help>\n+ <![CDATA[\n+\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.\n+\n+Input data: \n+\n+- MSI data as imzML or file (upload via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_\n+- or MSI data as peak list (tabular file) with the columns named "snr", "mass", "intensity" and "spectrum". To obtain a valid imzML output file spectrum should contain the pixel coordinates in the format: "x = 1, y = 1"\n+- optinal tabular file with pixel coordinates to restrict reading of imzML file to coordinates of interest\n+- optional tabular file with pixel annotations. The annotations can be used to summarize pixels of an imzML file which belong to the same group and detect peaks on average spectra, further steps will be done on average spectra as well and average spectra are exported. If this option was not chosen the filtering tool can use the annotations to filter for peaks within pixel groups (select "Group wise filtering")\n+\n+\n+Options:\n+\n+- Peak detection: detection of peaks, only possible with imzML input\n+- Monoisotopic peaks: detection of monoisotopic peaks\n+- Peak binning: After the alignment the peak positions (mass) are very similar but not identical. The binning is needed to make similar peak mass values identical.\n+- Peak filtering: Removal of less frequent peaks (either with a minimum ratio or with an absolute minimum number of spectra in which the peak has to occur)\n+\n+\n+Output: \n+\n+- centroided processed or continuous imzML file\n+- pdf with mass spectra after each preprocessing step\n+- peak list (tabular file) with the columns "snr", "mass", "intensity" and "spectrum"\n+- tabular file with intensity matrix (m/z in rows and spectra in columns). If the input file was imzML in profile mode the intensities before peak picking are also stored in the matrix . For all other inputs not picked values are set to NA. \n+\n+.. _MALDIquant: http://strimmerlab.org/software/maldiquant/\n+\n+ ]]>\n+ </help>\n+ <expand macro="citation"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 01212bf66f61 test-data/Example_Continuous.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Example_Continuous.imzML Wed Aug 22 11:49:29 2018 -0400 |
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| diff -r 000000000000 -r 01212bf66f61 test-data/int1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/int1.tabular Wed Aug 22 11:49:29 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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| b |
| diff -r 000000000000 -r 01212bf66f61 test-data/intensity_matrix3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/intensity_matrix3.tabular Wed Aug 22 11:49:29 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 01212bf66f61 test-data/masspeaks1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masspeaks1.tabular Wed Aug 22 11:49:29 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 01212bf66f61 test-data/masspeaks1_forinput.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masspeaks1_forinput.tabular Wed Aug 22 11:49:29 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 01212bf66f61 test-data/masspeaks3.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masspeaks3.tabular Wed Aug 22 11:49:29 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 01212bf66f61 test-data/outfile1.ibd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outfile1.ibd Wed Aug 22 11:49:29 2018 -0400 |
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| diff -r 000000000000 -r 01212bf66f61 test-data/outfile1.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outfile1.imzML Wed Aug 22 11:49:29 2018 -0400 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 84 +-rw-r--r-- 1 meli meli 67160 Aug 22 13:56 ibd +-rw-r--r-- 1 meli meli 15071 Aug 22 13:56 imzml |
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| diff -r 000000000000 -r 01212bf66f61 test-data/outfile2.ibd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outfile2.ibd Wed Aug 22 11:49:29 2018 -0400 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 276 +-rw-r--r-- 1 meli meli 268784 Aug 22 13:56 ibd +-rw-r--r-- 1 meli meli 9286 Aug 22 13:56 imzml |
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| diff -r 000000000000 -r 01212bf66f61 test-data/outfile2.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outfile2.imzML Wed Aug 22 11:49:29 2018 -0400 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 276 +-rw-r--r-- 1 meli meli 268784 Aug 22 13:56 ibd +-rw-r--r-- 1 meli meli 9286 Aug 22 13:56 imzml |
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| diff -r 000000000000 -r 01212bf66f61 test-data/outfile3.ibd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outfile3.ibd Wed Aug 22 11:49:29 2018 -0400 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 52 +-rw-r--r-- 1 meli meli 38384 Aug 22 13:57 ibd +-rw-r--r-- 1 meli meli 9551 Aug 22 13:57 imzml |
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| diff -r 000000000000 -r 01212bf66f61 test-data/outfile3.imzML --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outfile3.imzML Wed Aug 22 11:49:29 2018 -0400 |
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| @@ -0,0 +1,4 @@ +imzML file: +total 52 +-rw-r--r-- 1 meli meli 38384 Aug 22 13:57 ibd +-rw-r--r-- 1 meli meli 9551 Aug 22 13:57 imzml |
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| diff -r 000000000000 -r 01212bf66f61 test-data/pixel_annotations.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pixel_annotations.tabular Wed Aug 22 11:49:29 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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| diff -r 000000000000 -r 01212bf66f61 test-data/restricted_pixels.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/restricted_pixels.tabular Wed Aug 22 11:49:29 2018 -0400 |
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