| Previous changeset 11:0159b15b1281 (2020-10-06) Next changeset 13:cc430977c8ff (2020-12-23) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 39bd480e8813fa7a96b640150365577a69885d17-dirty" |
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modified:
segmentation.xml 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/centroids_proc.pdf test-data/preprocessing_results1.ibd test-data/preprocessing_results1.imzml test-data/preprocessing_results1.imzml.txt test-data/preprocessing_results1.pdf test-data/preprocessing_results2.ibd test-data/preprocessing_results2.imzml test-data/preprocessing_results2.imzml.txt test-data/preprocessing_results2.pdf test-data/preprocessing_results3.ibd test-data/preprocessing_results3.imzml test-data/preprocessing_results3.imzml.txt test-data/preprocessing_results3.pdf |
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| diff -r 0159b15b1281 -r 050bcc806da2 segmentation.xml --- a/segmentation.xml Tue Oct 06 08:04:35 2020 +0000 +++ b/segmentation.xml Sun Nov 29 23:37:41 2020 +0000 |
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| @@ -381,14 +381,11 @@ <output name="pixeloutput" file="classes_ssc.tabular"/> </test> <test> - <param name="infile" value="" ftype="imzml"> - <composite_data value="preprocessing_results3.imzml"/> - <composite_data value="preprocessing_results3.ibd"/> - </param> + <expand macro="processed_infile_imzml"/> <conditional name="processed_cond"> <param name="processed_file" value="processed"/> - <param name="accuracy" value="1"/> - <param name="units" value="mz"/> + <param name="accuracy" value="200"/> + <param name="units" value="ppm"/> </conditional> <param name="segmentationtool" value="centroids"/> <param name="centroids_r" value="1"/> @@ -408,10 +405,10 @@ <output name="pixeloutput" file="classes_proc.tabular"/> <output name="mzfeatures"> <assert_contents> - <has_text text="1212" /> - <has_text text="1297" /> - <has_text text="1199" /> - <has_text text="1298" /> + <has_text text="100.642" /> + <has_text text="101.816297645089" /> + <has_text text="1.34687866193417" /> + <has_text text="6.43855724908388" /> <has_n_columns n="9" /> <has_n_lines n="101" /> </assert_contents> |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/Heatmaps_LM8_file16.pdf |
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| Binary file test-data/Heatmaps_LM8_file16.pdf has changed |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/Heatmaps_analyze75.pdf |
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| Binary file test-data/Heatmaps_analyze75.pdf has changed |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/Heatmaps_imzml.pdf |
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| Binary file test-data/Heatmaps_imzml.pdf has changed |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/Heatmaps_processed.pdf |
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| Binary file test-data/Heatmaps_processed.pdf has changed |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/Heatmaps_rdata.pdf |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/centroids_proc.pdf |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results1.ibd |
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| Binary file test-data/preprocessing_results1.ibd has changed |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results1.imzml --- a/test-data/preprocessing_results1.imzml Tue Oct 06 08:04:35 2020 +0000 +++ b/test-data/preprocessing_results1.imzml Sun Nov 29 23:37:41 2020 +0000 |
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| 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:1000127" name="centroid spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="07177fdd-3760-4df6-8fe2-53d28b280ae8" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="749fe32c8243da06001cf4643c5ce4f1ef5a98a8" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="22bd3147-231d-4076-b6bd-67c1fa7c6ef3" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="831eba0fc850529d1351bcbb1baf779fe0773e1b" />\n \t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n@@ -86,15 +86,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="36" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="48" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -115,15 +115,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="56" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="80" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -144,15 +144,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="exter'..b'upRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="156" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="240" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -289,15 +289,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="176" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="272" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n@@ -318,15 +318,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="196" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="5" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="20" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="304" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="8" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="32" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t</binaryDataArrayList>\n' |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results1.imzml.txt --- a/test-data/preprocessing_results1.imzml.txt Tue Oct 06 08:04:35 2020 +0000 +++ b/test-data/preprocessing_results1.imzml.txt Sun Nov 29 23:37:41 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-rw-r-- 1 meli meli 216 Oct 5 19:57 ibd --rw-rw-r-- 1 meli meli 18090 Oct 5 19:57 imzml +-rw-rw-r-- 1 meli meli 336 Nov 29 01:14 ibd +-rw-rw-r-- 1 meli meli 18092 Nov 29 01:14 imzml |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results1.pdf |
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| Binary file test-data/preprocessing_results1.pdf has changed |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results2.ibd |
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| Binary file test-data/preprocessing_results2.ibd has changed |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results2.imzml --- a/test-data/preprocessing_results2.imzml Tue Oct 06 08:04:35 2020 +0000 +++ b/test-data/preprocessing_results2.imzml Sun Nov 29 23:37:41 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:1000127" name="centroid spectrum" value="" /> - <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="503079b4-538a-4be6-b70d-e52542c66482" /> - <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="a597fe6a0184ef339105b3a932f58726a9af549b" /> + <cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="ebbd9c5a-19a7-4db5-91e0-858065743606" /> + <cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="471a838ffd01331ad8e6d23a59004e05745bf39c" /> <cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" /> </fileContent> </fileDescription> |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results2.imzml.txt --- a/test-data/preprocessing_results2.imzml.txt Tue Oct 06 08:04:35 2020 +0000 +++ b/test-data/preprocessing_results2.imzml.txt Sun Nov 29 23:37:41 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 64 --rw-rw-r-- 1 meli meli 37404 Oct 5 19:57 ibd --rw-rw-r-- 1 meli meli 22796 Oct 5 19:57 imzml +-rw-rw-r-- 1 meli meli 37404 Nov 29 18:03 ibd +-rw-rw-r-- 1 meli meli 22796 Nov 29 18:03 imzml |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results2.pdf |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results3.ibd |
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| Binary file test-data/preprocessing_results3.ibd has changed |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results3.imzml --- a/test-data/preprocessing_results3.imzml Tue Oct 06 08:04:35 2020 +0000 +++ b/test-data/preprocessing_results3.imzml Sun Nov 29 23:37:41 2020 +0000 |
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| b'@@ -9,9 +9,9 @@\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:1000127" name="centroid spectrum" value="" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="be549a7e-87af-4413-9b4c-27221f55ee9a" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="4ee7ca6fb3f60e1adbe196068f86bc3209bace58" />\n-\t\t\t<cvParam cvRef="IMS" accession="IMS:1000031" name="processed" value="" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000080" name="universally unique identifier" value="476b127d-a8e1-4595-aae9-e9245db50d28" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000091" name="ibd SHA-1" value="8a36ea2658fcfc8cfa9ae4d0dd73cd7ed2f5b96f" />\n+\t\t\t<cvParam cvRef="IMS" accession="IMS:1000030" name="continuous" value="" />\n \t\t</fileContent>\n \t</fileDescription>\n \t<referenceableParamGroupList count="4">\n@@ -86,15 +86,15 @@\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="mzArray" />\n \t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="16" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="64" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="36" />\n+\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000104" name="external encoded length" value="144" />\n \t\t\t\t\t\t<binary />\n \t\t\t\t\t</binaryDataArray>\n \t\t\t\t\t<binaryDataArray encodedLength="0">\n \t\t\t\t\t\t<referenceableParamGroupRef ref="intensityArray" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000102" name="external offset" value="80" />\n-\t\t\t\t\t\t<cvParam cvRef="IMS" accession="IMS:1000103" name="external array length" value="16" 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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results3.imzml.txt --- a/test-data/preprocessing_results3.imzml.txt Tue Oct 06 08:04:35 2020 +0000 +++ b/test-data/preprocessing_results3.imzml.txt Sun Nov 29 23:37:41 2020 +0000 |
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| @@ -1,4 +1,4 @@ imzML file: total 24 --rw-rw-r-- 1 meli meli 960 Oct 5 19:58 ibd --rw-rw-r-- 1 meli meli 18112 Oct 5 19:58 imzml +-rw-rw-r-- 1 meli meli 1456 Nov 29 18:04 ibd +-rw-rw-r-- 1 meli meli 18133 Nov 29 18:04 imzml |
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| diff -r 0159b15b1281 -r 050bcc806da2 test-data/preprocessing_results3.pdf |
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| Binary file test-data/preprocessing_results3.pdf has changed |