| Previous changeset 8:87bb011a4ee8 (2020-05-13) Next changeset 10:5abc3ab4792c (2020-09-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 6e8b69ee3aff3c93f745a5de11cc9169130f2e5e" |
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modified:
macros.xml preprocessing.xml 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_combined.ibd test-data/123_combined.imzml test-data/123_combined.imzml.txt 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_combined.ibd test-data/12_combined.imzml test-data/12_combined.imzml.txt test-data/12_combined_QC.pdf test-data/2123_auto_combined.ibd test-data/2123_auto_combined.imzml test-data/2123_auto_combined.imzml.txt test-data/2123_auto_combined_QC.pdf test-data/Heatmaps_LM8_file16.pdf test-data/Heatmaps_analyze75.pdf test-data/Heatmaps_imzml.pdf test-data/Heatmaps_processed.pdf test-data/Heatmaps_rdata.pdf test-data/Plot_analyze75.pdf test-data/Plot_analyze75_allpixels.pdf test-data/Plot_imzml.pdf test-data/Plot_picked.pdf test-data/Plot_processed.pdf test-data/Plot_rdata.pdf test-data/QC_analyze75.pdf test-data/QC_empty_spectra.pdf test-data/QC_imzml.pdf test-data/QC_rdata.pdf test-data/analyze75_filtered2.pdf test-data/centroids_proc.pdf test-data/centroids_rdata.pdf test-data/cluster_skm.RData test-data/imzml_filtered3.pdf test-data/imzml_filtered4.pdf test-data/imzml_filtered5.pdf test-data/imzml_filtered8.pdf test-data/kmeans_analyze.pdf test-data/out3.ibd test-data/out3.imzml test-data/out3.imzml.txt test-data/out4.ibd test-data/out4.imzml test-data/out4.imzml.txt test-data/out5.ibd test-data/out5.imzml test-data/out5.imzml.txt test-data/out6.ibd test-data/out6.imzml test-data/out6.imzml.txt test-data/out7.ibd test-data/out7.imzml test-data/out7.imzml.txt test-data/out8.ibd test-data/out8.imzml test-data/out8.imzml.txt test-data/pca_imzml.pdf test-data/picked.ibd test-data/picked.imzml test-data/picked.imzml.txt test-data/picked_QC.pdf test-data/preprocessing_results4.imzml test-data/preprocessing_results4.imzml.txt test-data/preprocessing_results4.pdf test-data/rdata_notfiltered.pdf test-data/test1.pdf test-data/test2.pdf test-data/test2.rdata test-data/test3.pdf test-data/test4.pdf test-data/test4.rdata test-data/test5.pdf test-data/test6.pdf test-data/test6.rdata test-data/test7.pdf test-data/test7.rdata |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 macros.xml --- a/macros.xml Wed May 13 14:21:48 2020 -0400 +++ b/macros.xml Thu Sep 24 11:43:31 2020 +0000 |
| [ |
| @@ -1,10 +1,10 @@ <macros> - <token name="@VERSION@">2.4.0</token> + <token name="@VERSION@">2.6.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">bioconductor-cardinal</requirement> - <requirement type="package" version="3.6.1">r-base</requirement> + <!--requirement type="package" version="3.6.1">r-base</requirement--> <yield/> </requirements> </xml> @@ -175,7 +175,7 @@ - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_ - Analyze7.5 (upload hdr, img and t2m file via the "composite" function) - - Cardinal "MSImageSet" data saved as .RData + - Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData ]]></token> <token name="@MZ_TABULAR_INPUT_DESCRIPTION@"><![CDATA[ - Optional tabular file with m/z values: @@ -243,7 +243,7 @@ </param> <when value="no_processed"/> <when value="processed"> - <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/> + <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned"/> <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm"> <option value="mz" >mz</option> <option value="ppm" selected="True" >ppm</option> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 preprocessing.xml --- a/preprocessing.xml Wed May 13 14:21:48 2020 -0400 +++ b/preprocessing.xml Thu Sep 24 11:43:31 2020 +0000 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.2">\n+<tool id="cardinal_preprocessing" name="MSI preprocessing" version="@VERSION@.0">\n <description>\n mass spectrometry imaging preprocessing\n </description>\n@@ -7,7 +7,7 @@\n </macros>\n <expand macro="requirements">\n <requirement type="package" version="2.3">r-gridextra</requirement>\n- <requirement type="package" version="3.2.1">r-ggplot2</requirement>\n+ <requirement type="package" version="3.3.2">r-ggplot2</requirement>\n </expand>\n <command detect_errors="exit_code">\n <![CDATA[\n@@ -347,35 +347,37 @@\n title("Spectra after peak binning", outer=TRUE, line=0)\n \n \n- ############################### Data reduction ###########################\n+ ############################### Mass binning ###########################\n \n- #elif str( $method.methods_conditional.preprocessing_method) == \'Data_reduction\':\n- print(\'Data_reduction\')\n+ #elif str( $method.methods_conditional.preprocessing_method) == \'Mass_binning\':\n+ print(\'mass binning\')\n \n- ## these functions only work on MSImageSet\n- msidata = as(msidata, "MSImageSet")\n+ #if str( $method.methods_conditional.mz_range.features_filtering) == \'change_mz_range\':\n+\n+ #if str($processed_cond.processed_file) == "processed":\n \n- #if str( $method.methods_conditional.methods_for_reduction.reduction_method) == \'bin\':\n- print(\'bin reduction\')\n+ msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, from=$method.methods_conditional.mz_range.min_mz, to=$method.methods_conditional.mz_range.max_mz, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)\n+ \n+ #else \n+ msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)\n+ #end if\n+\n+\t\t \n+\t #elif str( $method.methods_conditional.mz_range.features_filtering) == \'none\':\t \n \n- msidata = reduceDimension(msidata, method="bin", width=$method.methods_conditional.methods_for_reduction.bin_width, units="$method.methods_conditional.methods_for_reduction.bin_units", fun=$method.methods_conditional.methods_for_reduction.bin_fun)\n+ msidata = mse_bin = mzBin(msidata,resolution=$method.methods_conditional.bin_width, units="$method.methods_conditional.bin_units", fun=$method.methods_conditional.bin_fun)\n \n+ #end if\n+ \n+ msidata <- process(msidata, BPPARAM=MulticoreParam(workers=number_cpu))\n+ \n ## optional: replace NA with 0\n- #if $method.methods_conditional.methods_for_reduction.replace_NA_bin:\n+ #if $method.methods_conditional.replace_NA_bin:\n ## count and replace NAs\n print(paste0("Number of NA that were set to zero after binning:",sum(is.na(spectra(msidata)))))\n spectra(msidata)[is.na(spectra(msidata))] = 0 \n #end if\n-\n- #elif str( $method.methods_conditional.methods_for_reduction.reduction_method) == \'resample\':\n- print(\'resample reduction\')\n-\n- msidata = reduceDimension(msidata, method="resample", step=$method.methods_conditional.methods_for_reduction.resample_step)\n- #end if\n-\n- ## coercition into new format\n- msidata = as(msidata, "MSImagingExperiment")\n-\n+ \n ############################### QC ###########################\n \n maxfeatures =nrow(msidata)\n@@ -386,7 +388,7 @@\n QC_numbers= cbind(QC_numbers, reduced)\n vectorofactions = append(vectorofactions, "reduced")\n print(plot(msidata, '..b'aram>\n+ <param name="bin_fun" type="select" display="radio"\n+ label="Calculate sum or mean intensity for ions of the same bin">\n+ <option value="mean" selected="True">mean</option>\n+ <option value="sum">sum</option>\n+ </param>\n+ <param name="replace_NA_bin" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Binning can introduce NAs, should they be replaced with 0"/>\n+ <conditional name="mz_range">\n+ \t\t <param name="features_filtering" type="select" label="Select m/z feature filtering option">\n+ <option value="none" selected="True">none</option>\n+ <option value="change_mz_range">change m/z range</option>\n </param>\n- <when value="bin">\n- <param name="bin_width" type="float" value="1"\n- label="The width of a bin in m/z or ppm" help="Width must be greater than range of m/z values divided by number of m/z features"/>\n- <param name="bin_units" type="select" display="radio"\n- label="Unit for bin">\n- <option value="mz" selected="True">mz</option>\n- <option value="ppm">ppm</option>\n- </param>\n- <param name="bin_fun" type="select" display="radio"\n- label="Calculate sum or mean intensity for ions of the same bin">\n- <option value="mean" selected="True">mean</option>\n- <option value="sum">sum</option>\n- </param>\n- <param name="replace_NA_bin" type="boolean" label="Replace NA with 0" truevalue="TRUE" falsevalue="FALSE" checked="True" help="Binning can introduce NAs, should they be replaced with 0"/>\n- </when>\n- <when value="resample">\n- <param name="resample_step" type="float" value="1"\n- label="The step size in m/z" help="Step size must be greater than range of m/z values divided by number of m/z features"/>\n- </when>\n+\t\t\t <when value="none"/>\n+\t\t\t <when value="change_mz_range">\n+\t\t\t\t<param name="min_mz" type="float" value="1" label="Minimum value for m/z"/>\n+\t\t\t\t<param name="max_mz" type="float" value="10000" label="Maximum value for m/z"/>\n+\t\t\t </when>\n </conditional>\n </when>\n <when value="Transformation">\n@@ -800,11 +800,9 @@\n </repeat>\n <repeat name="methods">\n <conditional name="methods_conditional">\n- <param name="preprocessing_method" value="Data_reduction"/>\n- <conditional name="methods_for_reduction">\n- <param name="reduction_method" value="bin"/>\n+ <param name="preprocessing_method" value="Mass_binning"/>\n <param name="bin_width" value="0.1"/>\n- </conditional>\n+ <param name="bin_units" value="mz"/>\n </conditional>\n </repeat>\n <output name="QC_overview" file="preprocessing_results4.pdf" compare="sim_size"/>\n@@ -817,7 +815,7 @@\n <expand macro="processed_infile_imzml"/>\n <conditional name="processed_cond">\n <param name="processed_file" value="processed"/>\n- <param name="accuracy" value="100"/>\n+ <param name="accuracy" value="200"/>\n <param name="units" value="ppm"/>\n </conditional>\n <repeat name="methods">\n' |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/112_auto_combined.ibd |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/112_auto_combined.imzml --- a/test-data/112_auto_combined.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/112_auto_combined.imzml Thu Sep 24 11:43:31 2020 +0000 |
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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="de720b1f-c3fa-4596-b054-284efaff29fc" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="040b9782d76e25ebe9a6b7c27fdda7e27e711674" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="23f1e1c8-aaa5-4d04-ab81-da14f7d24507" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="b2e009b6e72791420e704b751b4fc1a0f36bf420" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/112_auto_combined.imzml.txt --- a/test-data/112_auto_combined.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/112_auto_combined.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 556 --rw-r--r-- 1 meli meli 537552 Apr 21 12:46 ibd --rw-r--r-- 1 meli meli 27497 Apr 21 12:46 imzml +-rw-rw-r-- 1 meli meli 537552 Aug 30 13:50 ibd +-rw-rw-r-- 1 meli meli 27497 Aug 30 13:50 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/112_auto_combined_QC.pdf |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/123_combined.ibd |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/123_combined.imzml --- a/test-data/123_combined.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/123_combined.imzml Thu Sep 24 11:43:31 2020 +0000 |
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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="c9f19079-a92c-4995-b4ee-48d2766994a8" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="889b1020d3d844330f13a360be4b2bd0b65d11a1" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="383dcc6e-fa4e-4ffe-8523-9cd0c3bd2571" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2cd98028c7ab9bd53b698168b508a0ac74f256c9" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/123_combined.imzml.txt --- a/test-data/123_combined.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/123_combined.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 452 --rw-r--r-- 1 meli meli 436764 Apr 21 12:41 ibd --rw-r--r-- 1 meli meli 22855 Apr 21 12:41 imzml +-rw-rw-r-- 1 meli meli 436764 Aug 30 13:46 ibd +-rw-rw-r-- 1 meli meli 22855 Aug 30 13:46 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/123_combined_QC.pdf |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/123_combined_auto.ibd |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/123_combined_auto.imzml --- a/test-data/123_combined_auto.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/123_combined_auto.imzml Thu Sep 24 11:43:31 2020 +0000 |
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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="386d1a7c-e065-4bf1-96a6-019586133b29" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9bdafd878211e7d0c8fd0ef11bd534cbacfe7d40" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="ae23e625-6ac2-4a33-be4a-b73af67bc0dd" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="1b81e4b14567ea9da1177c0490f636d0823b2aac" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/123_combined_auto.imzml.txt --- a/test-data/123_combined_auto.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/123_combined_auto.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 452 --rw-r--r-- 1 meli meli 436764 Apr 21 12:43 ibd --rw-r--r-- 1 meli meli 22860 Apr 21 12:43 imzml +-rw-rw-r-- 1 meli meli 436764 Aug 30 13:48 ibd +-rw-rw-r-- 1 meli meli 22860 Aug 30 13:48 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/123_combined_auto.pdf |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/12_combined.imzml --- a/test-data/12_combined.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/12_combined.imzml Thu Sep 24 11:43:31 2020 +0000 |
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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="57f26041-833d-4843-ba25-0037f2c35f51" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="c271b37214900da9960cd3bcb748cc5bc377cfec" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="85ec7820-8e87-4fb2-b74a-5b9cd8cf24d6" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d8a4e14091441873e8969f3b6b249f55b4d95146" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/12_combined.imzml.txt --- a/test-data/12_combined.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/12_combined.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 352 --rw-r--r-- 1 meli meli 335976 Apr 21 12:45 ibd --rw-r--r-- 1 meli meli 18225 Apr 21 12:45 imzml +-rw-rw-r-- 1 meli meli 335976 Aug 30 13:49 ibd +-rw-rw-r-- 1 meli meli 18225 Aug 30 13:49 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/2123_auto_combined.imzml --- a/test-data/2123_auto_combined.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/2123_auto_combined.imzml Thu Sep 24 11:43:31 2020 +0000 |
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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="1c0a127a-8417-47ef-a049-553b9d56de81" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="5113bf7d09e0b1a584238aa6c5242f50eeef839b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="d5abe155-9afd-4249-aaf3-8fc631c1fd10" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="3c93096f299dc50ca088d712feca19f8bf2d5152" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/2123_auto_combined.imzml.txt --- a/test-data/2123_auto_combined.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/2123_auto_combined.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 656 --rw-r--r-- 1 meli meli 638340 Apr 21 12:46 ibd --rw-r--r-- 1 meli meli 32132 Apr 21 12:46 imzml +-rw-rw-r-- 1 meli meli 638340 Aug 30 13:50 ibd +-rw-rw-r-- 1 meli meli 32132 Aug 30 13:50 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out3.imzml --- a/test-data/out3.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out3.imzml Thu Sep 24 11:43:31 2020 +0000 |
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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="7cde7a72-9a6b-4ed9-a809-79ca20bf45b4" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4a26497a6ddfc9a61e9c0e463e4c246c5d734f80" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="c6cc990a-d910-4c17-aedd-ceb204b4d105" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ef8c4f864d0386736c986ebb4d4eb29a726e42d4" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out3.imzml.txt --- a/test-data/out3.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out3.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-r--r-- 1 meli meli 9616 Mär 24 20:25 ibd --rw-r--r-- 1 meli meli 8958 Mär 24 20:25 imzml +-rw-rw-r-- 1 meli meli 9616 Aug 23 17:39 ibd +-rw-rw-r-- 1 meli meli 8958 Aug 23 17:39 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out4.imzml --- a/test-data/out4.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out4.imzml Thu Sep 24 11:43:31 2020 +0000 |
| b |
| @@ -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="b0dec95e-b66f-4c3f-86df-166d942f42c3" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="d9b557cf2c0e15a0cdd863e50897b07a55a26f31" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="78fa5a7c-8dc8-4ff1-ad77-b19714f285cb" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="64d40f8c65af1399e24d94569f4dd3fdbf43a901" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out4.imzml.txt --- a/test-data/out4.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out4.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ imzML file: total 44 --rw-r--r-- 1 meli meli 28792 Mär 24 19:23 ibd --rw-r--r-- 1 meli meli 12046 Mär 24 19:23 imzml +-rw-rw-r-- 1 meli meli 28792 Aug 23 17:39 ibd +-rw-rw-r-- 1 meli meli 12046 Aug 23 17:39 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out5.imzml --- a/test-data/out5.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out5.imzml Thu Sep 24 11:43:31 2020 +0000 |
| b |
| @@ -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="87b0ab73-abe6-4eb6-91ba-b6d493a343bc" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="9de3a02d0943ecda0717845511a8f7b8f58d1db7" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="30751422-deca-429e-9f8e-24639c108d6d" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="2c7f19c6447844039a112152c19f7cfd50dbf12e" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out5.imzml.txt --- a/test-data/out5.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out5.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ imzML file: total 20 --rw-r--r-- 1 meli meli 380 Mär 24 19:24 ibd --rw-r--r-- 1 meli meli 13525 Mär 24 19:24 imzml +-rw-rw-r-- 1 meli meli 380 Aug 23 17:40 ibd +-rw-rw-r-- 1 meli meli 13525 Aug 23 17:40 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out6.imzml --- a/test-data/out6.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out6.imzml Thu Sep 24 11:43:31 2020 +0000 |
| b |
| @@ -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="8b625a26-987e-4e32-b7d4-729efe840814" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="78e6eb56507d789575ee0495e60f9d44a192c0dd" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="254b991f-92f5-46d5-8069-6f9ecd53b05a" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="0aaa784dc2a335da176a4bc2d12a43f2d18bdbf1" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out6.imzml.txt --- a/test-data/out6.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out6.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ imzML file: total 164 --rw-r--r-- 1 meli meli 146896 Mär 24 19:25 ibd --rw-r--r-- 1 meli meli 18221 Mär 24 19:25 imzml +-rw-rw-r-- 1 meli meli 146896 Aug 23 17:41 ibd +-rw-rw-r-- 1 meli meli 18221 Aug 23 17:41 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out7.imzml --- a/test-data/out7.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out7.imzml Thu Sep 24 11:43:31 2020 +0000 |
| b |
| @@ -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="bf61653e-aa1a-4f9a-a84d-3ff3435ee7fe" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="352c33defde6728b7dfb83e18ed1c433fa4b8697" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="227ecc2e-a494-4018-afc5-45eaa790e812" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="e22162d1dd762607ca6d31c0b8892e0ae5a3a772" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out7.imzml.txt --- a/test-data/out7.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out7.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ imzML file: total 116 --rw-r--r-- 1 meli meli 95976 Mär 24 19:26 ibd --rw-r--r-- 1 meli meli 18199 Mär 24 19:26 imzml +-rw-rw-r-- 1 meli meli 95976 Aug 23 17:41 ibd +-rw-rw-r-- 1 meli meli 18199 Aug 23 17:41 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out8.imzml --- a/test-data/out8.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out8.imzml Thu Sep 24 11:43:31 2020 +0000 |
| b |
| @@ -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="ace74b18-25e2-4722-89f4-6eedc2b62ed8" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="41d580d8acf3e67df8b63f001fe941da7334861b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="91ed729b-0b8d-49f6-b832-e4d3834fe733" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="efd09bddeebeb334efe9dffad3a4f3bed35442d1" /> <cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" /> </fileContent> </fileDescription> @@ -42,7 +42,7 @@ </sample> </sampleList> <softwareList count="1"> - <software id="Cardinal" version="2.4.0"> + <software id="Cardinal" version="2.6.0"> <cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" /> </software> </softwareList> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/out8.imzml.txt --- a/test-data/out8.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/out8.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 348 --rw-r--r-- 1 meli meli 335976 Mär 24 19:27 ibd --rw-r--r-- 1 meli meli 12402 Mär 24 19:27 imzml +-rw-rw-r-- 1 meli meli 335976 Aug 23 17:42 ibd +-rw-rw-r-- 1 meli meli 12402 Aug 23 17:42 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/picked.ibd |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/picked.imzml --- a/test-data/picked.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/picked.imzml Thu Sep 24 11:43:31 2020 +0000 |
| b |
| @@ -8,8 +8,8 @@ <fileDescription> <fileContent> <cvParam cvRef="MS" accession="MS:1000579" name="MS1 spectrum"/> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{cb7c9edc-eee3-4159-a8a1-efdf5fc56a13}"/> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="f3e61f4699108e65bb678cfbbd6208be562f11c9"/> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="{19bd2a62-4cc1-4316-b173-25f1de3871f6}"/> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="ca84032e28aa3c04e4f41b74b85ccd1bd6e44107"/> <cvParam cvRef="IMS" accession="IMS:1000031" name="processed"/> <userParam name="MALDIquantForeign" value="MALDIquant object(s) exported to mzML"/> </fileContent> |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/picked.imzml.txt --- a/test-data/picked.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/picked.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 192 --rw-r--r-- 1 meli meli 157984 Apr 21 12:42 ibd --rw-r--r-- 1 meli meli 35012 Apr 21 12:42 imzml +-rw-rw-r-- 1 meli meli 157984 Aug 30 13:47 ibd +-rw-rw-r-- 1 meli meli 35012 Aug 30 13:47 imzml |
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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/preprocessing_results4.imzml --- a/test-data/preprocessing_results4.imzml Wed May 13 14:21:48 2020 -0400 +++ b/test-data/preprocessing_results4.imzml Thu Sep 24 11:43:31 2020 +0000 |
| b |
| b'@@ -9,8 +9,8 @@\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 unique identifier" value="c6122884-ceb5-46b6-9160-5d28e8862946" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="03e4b58b8e63517605164e90b85fe93a851a9c5b" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="9a685278-3bf0-48b5-b7c7-73a7a92625b2" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="036c4b8bf3f2f5a42a223ffd0b895f08b0a65f36" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -42,7 +42,7 @@\n \t\t</sample>\n \t</sampleList>\n \t<softwareList count="1">\n-\t\t<software id="Cardinal" 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| diff -r 87bb011a4ee8 -r ca727a6dede6 test-data/preprocessing_results4.imzml.txt --- a/test-data/preprocessing_results4.imzml.txt Wed May 13 14:21:48 2020 -0400 +++ b/test-data/preprocessing_results4.imzml.txt Thu Sep 24 11:43:31 2020 +0000 |
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