| Previous changeset 1:7a4540275084 (2024-04-23) Next changeset 3:6b0fef8a77c0 (2024-05-30) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit b9574494a6f9d2239dc81899e6d4074b33b078b7 |
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modified:
isolib.R isolib.xml test-data/lc_markers_neg.tsv |
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added:
test-data/markers_no_rt.tsv test-data/test1.msp |
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| diff -r 7a4540275084 -r b3251a7dae25 isolib.R --- a/isolib.R Tue Apr 23 07:42:32 2024 +0000 +++ b/isolib.R Wed Apr 24 14:51:32 2024 +0000 |
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| @@ -2,6 +2,7 @@ library(Spectra) library(MsBackendMsp) library(MetaboCoreUtils) +library(readr) #' @param args A list of command line arguments. main <- function() { @@ -9,7 +10,11 @@ data(adducts) args <- commandArgs(trailingOnly = TRUE) - compound_table <- read.delim(args[1], stringsAsFactors = FALSE) + compound_table <- read_tsv( + file = args[1], + col_types = "ccd", + col_select = tidyselect::all_of(c("name", "formula")) | tidyselect::any_of("rt") + ) adducts_to_use <- c(unlist(strsplit(args[2], ",", fixed = TRUE))) chemforms <- compound_table$formula |
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| diff -r 7a4540275084 -r b3251a7dae25 isolib.xml --- a/isolib.xml Tue Apr 23 07:42:32 2024 +0000 +++ b/isolib.xml Wed Apr 24 14:51:32 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="isolib" name="isolib" version="1.0.0+galaxy1" profile="21.09"> +<tool id="isolib" name="isolib" version="1.0.1+galaxy0" profile="21.09"> <description>create an isotopic pattern library for given compounds and adducts</description> <creator> <person @@ -19,6 +19,7 @@ <requirement type="package" version="1.12.0">bioconductor-spectra</requirement> <requirement type="package" version="1.6.0">bioconductor-msbackendmsp</requirement> <requirement type="package" version="2.6">r-envipat</requirement> + <requirement type="package" version="2.1.5">r-readr</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ Rscript '${__tool_directory__}/isolib.R' '${input_file}' '${ionization.adducts}' '${threshold}' '${append_adduct}' '${isotope_library}' @@ -55,6 +56,10 @@ <param name="input_file" value="lc_markers_neg.tsv"/> <output name="isotope_library" file="test0.msp"/> </test> + <test> + <param name="input_file" value="markers_no_rt.tsv"/> + <output name="isotope_library" file="test1.msp"/> + </test> </tests> <help><![CDATA[ This tool computes isotopic patterns for given compounds and adduct forms. |
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| diff -r 7a4540275084 -r b3251a7dae25 test-data/lc_markers_neg.tsv --- a/test-data/lc_markers_neg.tsv Tue Apr 23 07:42:32 2024 +0000 +++ b/test-data/lc_markers_neg.tsv Wed Apr 24 14:51:32 2024 +0000 |
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| @@ -7,8 +7,8 @@ C6H5NO3 4-nitrophenol 165 C6H4Cl1N1O2 6-Chloronicotinic acid 172.2 C19H28N2O5S Acetochlor mercapturate 607.2 -C19H28N2O5S1 Alachlor mercapturate 607.2 -C10H12N2O3S1 Bentazone 747.6 +C19H28N2O5S1 Alachlor mercapturate "607.2" +C10H12N2O3S1 Bentazone "747.6" C4H11O3P1S1 Diethylthiophosphate 177 C14H17Cl2NO2 Fenhexamid 689.4 C11H13ClO2 Fenvalerate free acid 585 |
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| diff -r 7a4540275084 -r b3251a7dae25 test-data/markers_no_rt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/markers_no_rt.tsv Wed Apr 24 14:51:32 2024 +0000 |
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| @@ -0,0 +1,6 @@ +formula name +C8H6Cl2O3 2,4-Dichlorophenoxyacetic acid ou 2,4-D +C9H15N3O1 2-diethylamino-6-methyl pyrimidin-4-ol/one +C5H2Cl3N1O1 3,5,6-Trichloro-2-pyridinol +C13H10O3 3-phenoxybenzoic acid +C13H9FO3 4-Fluoro-3-phenoxybenzoic acid \ No newline at end of file |
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| diff -r 7a4540275084 -r b3251a7dae25 test-data/test1.msp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.msp Wed Apr 24 14:51:32 2024 +0000 |
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| @@ -0,0 +1,64 @@ +NAME: 2,4-Dichlorophenoxyacetic acid ou 2,4-D (M-H) +msLevel: MS1 +PRECURSORTYPE: [M-H]- +FORMULA: C8H6Cl2O3 +charge: -1 +ionization_mode: negative +precursor_mz: 218.962123412 +Num Peaks: 5 +218.962123019909 100 +219.965477859909 8.65258263418579 +220.959172909909 63.9915522703273 +221.962527749909 5.53692193908827 +222.956222799909 10.2372969049151 + +NAME: 2-diethylamino-6-methyl pyrimidin-4-ol/one (M-H) +msLevel: MS1 +PRECURSORTYPE: [M-H]- +FORMULA: C9H15N3O1 +charge: -1 +ionization_mode: negative +precursor_mz: 180.1142361 +Num Peaks: 3 +180.114235677909 100 +181.111270637909 1.09598940142117 +181.117590517909 9.73415546345901 + +NAME: 3,5,6-Trichloro-2-pyridinol (M-H) +msLevel: MS1 +PRECURSORTYPE: [M-H]- +FORMULA: C5H2Cl3N1O1 +charge: -1 +ionization_mode: negative +precursor_mz: 195.912920724 +Num Peaks: 7 +195.912920371909 100 +196.916275211909 5.40786414636612 +197.909970261909 95.987328405491 +198.913325101909 5.19086431789525 +199.907020151909 30.7118907147453 +200.910374991909 1.66085732663385 +201.904070041909 3.27550259998867 + +NAME: 3-phenoxybenzoic acid (M-H) +msLevel: MS1 +PRECURSORTYPE: [M-H]- +FORMULA: C13H10O3 +charge: -1 +ionization_mode: negative +precursor_mz: 213.05571818 +Num Peaks: 2 +213.055717727909 100 +214.059072567909 14.0604467805519 + +NAME: 4-Fluoro-3-phenoxybenzoic acid (M-H) +msLevel: MS1 +PRECURSORTYPE: [M-H]- +FORMULA: C13H9F1O3 +charge: -1 +ionization_mode: negative +precursor_mz: 231.046296368 +Num Peaks: 2 +231.046295895909 100 +232.049650735909 14.0604467805519 + |