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Merge pull request #29 from bigbio/dev
Move to thermorawfileparser to 2.0.0dev
2 parents 0318e0a + 169640e commit 226b107

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6 files changed

+121
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‎.gitignore‎

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@@ -199,10 +199,12 @@ testing/
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testing*/
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*.pyc
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.nf-test
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*nf.test.snap
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nf.test.snap
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# Codacy
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.codacy
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# IDEA
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.idea/
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.nf-test*

‎modules/bigbio/onsite/tests/main.nf.test.snap‎

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{
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"versions_phosphors": {
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"content": [
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[
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"versions.yml:md5,bafdb21e8e35a3f6128f4b8fb2f17fa6"
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]
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],
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"timestamp": "2026-03-22T22:19:06.163312",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.10.4"
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}
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},
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"versions_ascore": {
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"content": [
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[
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"versions.yml:md5,e0bda208d6e29ca106d701db6ff8c6c9"
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]
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],
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"timestamp": "2026-03-22T22:17:57.833213",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.10.4"
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}
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},
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"versions_stub": {
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"content": [
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[
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"versions.yml:md5,669fa42376f9ff6641abd22c67e507d6"
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]
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],
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"timestamp": "2026-03-22T22:25:52.844037",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.10.4"
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}
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},
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"versions_lucxor": {
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"content": [
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[
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"versions.yml:md5,669fa42376f9ff6641abd22c67e507d6"
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]
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],
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"timestamp": "2026-03-22T22:22:30.192671",
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"meta": {
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"nf-test": "0.9.5",
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"nextflow": "25.10.4"
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}
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}
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}

‎modules/bigbio/thermorawfileparser/environment.yml‎

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@@ -3,4 +3,4 @@ channels:
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- bioconda
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- defaults
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dependencies:
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- bioconda::thermorawfileparser=1.4.5
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- bioconda::thermorawfileparser=2.0.0.dev

‎modules/bigbio/thermorawfileparser/main.nf‎

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@@ -5,16 +5,16 @@ process THERMORAWFILEPARSER {
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label 'error_retry'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://depot.galaxyproject.org/singularity/thermorawfileparser:1.4.5--h05cac1d_1'
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: 'biocontainers/thermorawfileparser:1.4.5--h05cac1d_1'}"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/thermorawfileparser:2.0.0.dev--h9ee0642_0' :
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'biocontainers/thermorawfileparser:2.0.0.dev--h9ee0642_0' }"
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input:
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tuple val(meta), path(raw)
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output:
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tuple val(meta), path("*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}"), emit: spectra
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tuple val("${task.process}"), val('thermorawfileparser'), eval("ThermoRawFileParser.sh --version"), emit: versions_thermorawfileparser, topic: versions
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tuple val("${task.process}"), val('thermorawfileparser'), eval("thermorawfileparser --version"), emit: versions_thermorawfileparser, topic: versions
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path "*.log", emit: log
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when:
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suffix = args.contains("--gzip") ? "${suffix}.gz" : "${suffix}"
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"""
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ThermoRawFileParser.sh \\
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thermorawfileparser \\
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-i='${raw}' \\
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${formatArg} ${args} \\
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-o=./ 2>&1 | tee '${prefix}_conversion.log'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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ThermoRawFileParser: \$(ThermoRawFileParser.sh --version)
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ThermoRawFileParser: \$(thermorawfileparser --version)
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END_VERSIONS
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"""
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}

‎modules/bigbio/thermorawfileparser/tests/main.nf.test.snap‎

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[
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"THERMORAWFILEPARSER",
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"thermorawfileparser",
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"1.4.5"
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"2.0.0.0"
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]
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]
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],
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"timestamp": "2026-03-20T12:41:22.8183",
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"meta": {
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"nf-test": "0.9.4",
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"nextflow": "25.10.4"
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}
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"nf-test": "0.9.3",
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"nextflow": "25.04.6"
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},
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"timestamp": "2026-03-23T22:31:25.789483"
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},
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"versions": {
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"content": [
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[
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[
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"THERMORAWFILEPARSER",
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"thermorawfileparser",
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"1.4.5"
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"2.0.0.0"
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]
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]
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],
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"timestamp": "2026-03-20T12:36:30.88531",
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"meta": {
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"nf-test": "0.9.4",
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"nextflow": "25.10.4"
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}
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"nf-test": "0.9.3",
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"nextflow": "25.04.6"
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},
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"timestamp": "2026-03-23T22:29:04.754961"
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},
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"Should run stub mode": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test_sample",
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"mzml_id": "test_sample"
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},
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"test_sample.mzML:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"1": [
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[
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"THERMORAWFILEPARSER",
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"thermorawfileparser",
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"2.0.0.0"
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]
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],
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"2": [
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"test_sample_conversion.log:md5,d41d8cd98f00b204e9800998ecf8427e"
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],
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"log": [
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"test_sample_conversion.log:md5,d41d8cd98f00b204e9800998ecf8427e"
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],
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"spectra": [
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[
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{
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"id": "test_sample",
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"mzml_id": "test_sample"
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},
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"test_sample.mzML:md5,d41d8cd98f00b204e9800998ecf8427e"
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]
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],
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"versions_thermorawfileparser": [
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[
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"THERMORAWFILEPARSER",
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"thermorawfileparser",
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"2.0.0.0"
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]
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]
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}
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.04.6"
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},
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"timestamp": "2026-03-23T22:31:25.88765"
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}
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}

‎tests/config/test_data.config‎

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}
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onsite {
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// Test data for onsite PTM localization module
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// Using GitHub media links to download LFS files
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mzml = "https://media.githubusercontent.com/media/weizhongchun/test-data/main/data/1.mzML"
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idxml = "https://raw.githubusercontent.com/weizhongchun/test-data/main/data/1_consensus_fdr_filter_pep.idXML"
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mzml = "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/onsite/1.mzML"
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idxml = "https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/onsite/1_consensus_fdr_filter_pep.idXML"
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}
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}
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}

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