Repository 'msnbase_readmsdata'
hg clone https://toolshed.g2.bx.psu.edu/repos/lecorguille/msnbase_readmsdata

Changeset 17:6de175c1f6ef (2024-07-15)
Previous changeset 16:12def6edac2f (2023-11-21)
Commit message:
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit eca29d4347fe2f4802091c4a06715232a6fd9253
added:
test-data/eic_plot.png
test-data/raw_plot.png
test-data/xcms_plot_eic_testdata.mzML
test-data/xcms_plot_raw_testdata.mzML
b
diff -r 12def6edac2f -r 6de175c1f6ef test-data/eic_plot.png
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Binary file test-data/eic_plot.png has changed
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diff -r 12def6edac2f -r 6de175c1f6ef test-data/raw_plot.png
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Binary file test-data/raw_plot.png has changed
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diff -r 12def6edac2f -r 6de175c1f6ef test-data/xcms_plot_eic_testdata.mzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xcms_plot_eic_testdata.mzML Mon Jul 15 16:03:15 2024 +0000
b
b'@@ -0,0 +1,3801 @@\n+<?xml version="1.0" encoding="ISO-8859-1"?>\n+<indexedmzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd">\n+<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd" accession="" version="1.1.0">\n+\t<cvList count="5">\n+\t\t<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"/>\n+\t\t<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo"/>\n+\t\t<cv id="BTO" fullName="BrendaTissue545" version="unknown" URI="http://www.brenda-enzymes.info/ontology/tissue/tree/update/update_files/BrendaTissueOBO"/>\n+\t\t<cv id="GO" fullName="Gene Ontology - Slim Versions" version="unknown" URI="http://www.geneontology.org/GO_slims/goslim_goa.obo"/>\n+\t\t<cv id="PATO" fullName="Quality ontology" version="unknown" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>\n+\t</cvList>\n+\t<fileDescription>\n+\t\t<fileContent>\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t</fileContent>\n+\t\t<sourceFileList count="1">\n+\t\t\t<sourceFile id="sf_ru_0" name="RCX_06_shortened.mzML" location="file:///C:/Users/473355/Downloads">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000569" name="SHA-1" value="6c9fc5a54e7e588b4940994f66c953de66f8e8c5" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000584" name="mzML format" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000777" name="spectrum identifier nativeID format" />\n+\t\t\t</sourceFile>\n+\t\t</sourceFileList>\n+\t</fileDescription>\n+\t<sampleList count="1">\n+\t\t<sample id="sa_0" name="">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000004" name="sample mass" value="0" unitAccession="UO:0000021" unitName="gram" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000005" name="sample volume" value="0" unitAccession="UO:0000098" unitName="milliliter" unitCvRef="UO" />\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000006" name="sample concentration" value="0" unitAccession="UO:0000175" unitName="gram per liter" unitCvRef="UO" />\n+\t\t</sample>\n+\t</sampleList>\n+\t<softwareList count="2">\n+\t\t<software id="so_in_0" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t\t<software id="so_default" version="" >\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000799" name="custom unreleased software tool" value="" />\n+\t\t</software>\n+\t</softwareList>\n+\t<instrumentConfigurationList count="1">\n+\t\t<instrumentConfiguration id="ic_0">\n+\t\t\t<cvParam cvRef="MS" accession="MS:1000031" name="instrument model" />\n+\t\t\t<softwareRef ref="so_in_0" />\n+\t\t</instrumentConfiguration>\n+\t</instrumentConfigurationList>\n+\t<dataProcessingList count="1">\n+\t\t<dataProcessing id="dp_sp_0">\n+\t\t\t<processingMethod order="0" softwareRef="so_default">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000544" name="Conversion to mzML" />\n+\t\t\t\t<userParam name="warning" type="xsd:string" value="fictional processing method used to fulfill format requirements" />\n+\t\t\t</processingMethod>\n+\t\t</dataProcessing>\n+\t</dataProcessingList>\n+\t<run id="ru_0" defaultInstrumentConfigurationRef="ic_0" sampleRef="sa_0" defaultSourceFileRef="sf_ru_0">\n+\t\t<userParam name="mzml_id" type="xsd:string" value="MZmine mzML export"/>\n+\t\t<spectrumList count="101" defaultDataProcessingRef="dp_sp_0">\n+\t\t\t<spectrum id="scan=100" index="0" defaultArrayLength="17" dataProcessingRef="dp_sp_0">\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000128" name="profile spectrum" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000511" name="ms level" value="1" />\n+\t\t\t\t<cvParam cvRef="MS" accession="MS:1000294" name="mass spectrum" />\n+\t\t\t\t<cvParam cvRef="MS" accession='..b'ffset>\n+\t\t<offset idRef="scan=113">38074</offset>\n+\t\t<offset idRef="scan=114">40753</offset>\n+\t\t<offset idRef="scan=115">43395</offset>\n+\t\t<offset idRef="scan=116">46058</offset>\n+\t\t<offset idRef="scan=117">48750</offset>\n+\t\t<offset idRef="scan=118">51379</offset>\n+\t\t<offset idRef="scan=119">54043</offset>\n+\t\t<offset idRef="scan=120">56707</offset>\n+\t\t<offset idRef="scan=121">59339</offset>\n+\t\t<offset idRef="scan=122">61982</offset>\n+\t\t<offset idRef="scan=123">64626</offset>\n+\t\t<offset idRef="scan=124">67269</offset>\n+\t\t<offset idRef="scan=125">69947</offset>\n+\t\t<offset idRef="scan=126">72590</offset>\n+\t\t<offset idRef="scan=127">75205</offset>\n+\t\t<offset idRef="scan=128">77800</offset>\n+\t\t<offset idRef="scan=129">80395</offset>\n+\t\t<offset id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diff -r 12def6edac2f -r 6de175c1f6ef test-data/xcms_plot_raw_testdata.mzML
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/xcms_plot_raw_testdata.mzML Mon Jul 15 16:03:15 2024 +0000
[
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