Mercurial > repos > workflow4metabolomics > ms2snoop
changeset 3:c68c94865667 draft
planemo upload commit 09540e3a13b630b078a35afd3e129bc18c9953f0
| author | workflow4metabolomics |
|---|---|
| date | Wed, 22 Jun 2022 13:07:01 +0000 |
| parents | a35fde23940e |
| children | 856001213966 |
| files | MS2snoop.R MS2snoop.xml README.md macros.xml test-data/compounds_pos.csv test-data/peaklist_precursors.csv |
| diffstat | 6 files changed, 3045 insertions(+), 33 deletions(-) [+] |
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--- a/MS2snoop.R Wed Jun 08 12:37:53 2022 +0000 +++ b/MS2snoop.R Wed Jun 22 13:07:01 2022 +0000 @@ -15,7 +15,7 @@ #' -assign("MS2SNOOP_VERSION", "1.0.1") +assign("MS2SNOOP_VERSION", "1.1.0") lockBinding("MS2SNOOP_VERSION", globalenv()) assign("MISSING_PARAMETER_ERROR", 1) @@ -202,10 +202,10 @@ c_name, min_number_scan, mzdecimal, - r_threshold=DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD, - seuil_ra=DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA, - tolmz=DEFAULT_EXTRACT_FRAGMENTS_TOLMZ, - tolrt=DEFAULT_EXTRACT_FRAGMENTS_TOLRT + r_threshold = DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD, + seuil_ra = DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA, + tolmz = DEFAULT_EXTRACT_FRAGMENTS_TOLMZ, + tolrt = DEFAULT_EXTRACT_FRAGMENTS_TOLRT ) { ## filter precursor in the precursors file based on mz and rt in the ## compound list @@ -252,6 +252,7 @@ if (global_verbose) { cat(" fragments :", vmz) + cat("\n") } ## mz of precursor in data precursor to check correlation with @@ -372,9 +373,6 @@ if (!is.null(res_comp_by_file)) { res_comp <- rbind(res_comp, res_comp_by_file) } - if (global_verbose) { - cat("\n") - } dev.off() } } else { @@ -625,6 +623,43 @@ } } +get_csv_or_tsv <- function( + path, + sep_stack = c("\t", ",", ";"), + header = TRUE, + quote = "\"" +) { + sep <- sep_stack[1] + result <- tryCatch({ + read.table( + file = path, + sep = sep, + header = header, + quote = quote + ) + }, error = function(e) { + return(data.frame()) + }) + if (length(sep_stack) == 1) { + return(result) + } + # if ( + # ncol(result) == 0 || ## failed + # ncol(result) == 1 ## only one row, suspicious, possible fail # nolint + # ) { + new_result <- get_csv_or_tsv( + path, + sep_stack = sep_stack[-1], + header = header, + quote = quote + ) + if (ncol(new_result) > ncol(result)) { + return(new_result) + } + # } + return(result) +} + main <- function(args) { if (args$version) { cat(sprintf("%s\n", MS2SNOOP_VERSION)) @@ -639,26 +674,11 @@ set_verbose() } ## MSpurity precursors file - precursors <- read.table( - file = args$precursors, - header = TRUE, - sep = "\t", - quote = "\"" - ) + precursors <- get_csv_or_tsv(args$precursors) ## MSpurity fragments file - fragments <- read.table( - file = args$fragments, - header = TRUE, - sep = "\t", - quote = "\"" - ) + fragments <- get_csv_or_tsv(args$fragments) ## list of compounds : col1=Name of molecule, col2=m/z, col3=retention time - compounds <- read.table( - file = args$compounds, - sep = "\t", - quote = "\"", - header = TRUE - ) + compounds <- get_csv_or_tsv(args$compounds) res_all <- NULL for (i in seq_len(nrow(compounds))) {
--- a/MS2snoop.xml Wed Jun 08 12:37:53 2022 +0000 +++ b/MS2snoop.xml Wed Jun 22 13:07:01 2022 +0000 @@ -3,8 +3,9 @@ MS1/MS2 spectra and associated adducts extraction and cleaning </description> <macros> - <token name="@TOOL_VERSION@">1.0.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <import>macros.xml</import> + <token name="@TOOL_VERSION@">1.1.0</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> <edam_topics> <edam_topic>topic_0091</edam_topic> @@ -50,20 +51,20 @@ <param argument="--compound_txt" type="data" - format="tabular,csv" + format="tabular,csv,tsv" label="list of compounds" help="The table must fit the format: col1=Name of molecule, col2=m/z, col3=retention time" /> <param argument="--peaklist_frag_tsv" type="data" - format="tabular,csv" + format="tabular,csv,tsv" label="MSpurity fragments file" /> <param argument="--peaklist_preco_tsv" type="data" - format="tabular,csv" + format="tabular,csv,tsv" label="MSpurity precursors file" /> <param @@ -150,6 +151,96 @@ <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> <output name="frag_result_txt" file="compound_fragments_result.txt" /> + <assert_stdout> + <expand macro="has_regular_stdout"/> + <expand macro="has_not_verbose_stdout"/> + <expand macro="has_not_debug_stdout"/> + </assert_stdout> + </test> + <test> + <param name="compound_txt" value="compounds_pos.txt" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> + <param name="verbose" value="--verbose" /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> + <assert_stdout> + <expand macro="has_regular_stdout"/> + <expand macro="has_verbose_stdout"/> + <expand macro="has_not_debug_stdout"/> + </assert_stdout> + </test> + <test> + <param name="compound_txt" value="compounds_pos.txt" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> + <param name="debug" value="--debug" /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> + <assert_stdout> + <expand macro="has_smol_stdout"/> + <expand macro="has_debug_stdout"/> + <expand macro="has_not_verbose_stdout"/> + </assert_stdout> + </test> + <test> + <param name="compound_txt" value="compounds_pos.txt" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.tsv" /> + <param name="debug" value="--debug" /> + <param name="verbose" value="--verbose" /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> + <assert_stdout> + <expand macro="has_smol_stdout"/> + <expand macro="has_debug_stdout"/> + <expand macro="has_smol_verbose_stdout"/> + </assert_stdout> + </test> + <test> + <param name="compound_txt" value="compounds_pos.csv" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> + <assert_stdout> + <expand macro="has_regular_stdout"/> + <expand macro="has_not_verbose_stdout"/> + <expand macro="has_not_debug_stdout"/> + </assert_stdout> + </test> + <test> + <param name="compound_txt" value="compounds_pos.csv" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> + <param name="verbose" value="--verbose" /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> + <assert_stdout> + <expand macro="has_regular_stdout"/> + <expand macro="has_verbose_stdout"/> + <expand macro="has_not_debug_stdout"/> + </assert_stdout> + </test> + <test> + <param name="compound_txt" value="compounds_pos.csv" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> + <param name="debug" value="--debug" /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> + <assert_stdout> + <expand macro="has_smol_stdout"/> + <expand macro="has_debug_stdout"/> + <expand macro="has_not_verbose_stdout"/> + </assert_stdout> + </test> + <test> + <param name="compound_txt" value="compounds_pos.csv" /> + <param name="peaklist_frag_tsv" value="peaklist_fragments.tsv" /> + <param name="peaklist_preco_tsv" value="peaklist_precursors.csv" /> + <param name="debug" value="--debug" /> + <param name="verbose" value="--verbose" /> + <output name="frag_result_txt" file="compound_fragments_result.txt" /> + <assert_stdout> + <expand macro="has_smol_stdout"/> + <expand macro="has_debug_stdout"/> + <expand macro="has_smol_verbose_stdout"/> + </assert_stdout> </test> </tests> <help><![CDATA[ @@ -163,7 +254,7 @@ ============== -MS2 validation +MS2 validation ============== -----------
--- a/README.md Wed Jun 08 12:37:53 2022 +0000 +++ b/README.md Wed Jun 22 13:07:01 2022 +0000 @@ -5,7 +5,7 @@ ----------- * **@name**: MS2 Snoop - * **@version**: 1.0.1 + * **@version**: 1.1.0 * **@authors**: Jean François Martin (INRAE) * **@maintainers**: Lain Pavot (PFEM - INRAE - MetaboHUB) * **@init date**: 2022, April
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jun 22 13:07:01 2022 +0000 @@ -0,0 +1,131 @@ +<macros> + + + <xml name="has_smol_stdout"> + <has_line line="processing 2-diethylamino-6-methyl pyrimidin-4-ol one " /> + <has_line line="processing 5-hydroxy-thiabendazole " /> + <has_line line="processing Tylosin " /> + </xml> + + <xml name="has_regular_stdout"> + <has_line line="processing 2-diethylamino-6-methyl pyrimidin-4-ol one " /> + <has_line line="processing 5-hydroxy-thiabendazole " /> + <has_line line="processing acetamiprid-N-desmethyl " /> + <has_line line="processing Acetochlor " /> + <has_line line="processing Avermectin B1a (Abamectin) " /> + <has_line line="processing Benzophenone-3 (Oxybenzone) " /> + <has_line line="processing Butocarboxim " /> + <has_line line="processing Carbendazim " /> + <has_line line="processing Cefoperazone " /> + <has_line line="processing Chlorfenvinphos " /> + <has_line line="processing Chlormequat " /> + <has_line line="processing Desisopropylatrazine " /> + <has_line line="processing Dichlorvos " /> + <has_line line="processing Dimethyldithiophosphate " /> + <has_line line="processing Emamectin B1a " /> + <has_line line="processing Fluopyram " /> + <has_line line="processing Hydroxy-tebuconazole " /> + <has_line line="processing Isoproturon " /> + <has_line line="processing Ivermectin B1a " /> + <has_line line="processing Malathion dicarboxilic acid " /> + <has_line line="processing Methamidophos " /> + <has_line line="processing Metolachlor " /> + <has_line line="processing N,N-diethyl-m-toluamide ou DEET " /> + <has_line line="processing Nigericin " /> + <has_line line="processing Omethoate " /> + <has_line line="processing Prochloraz " /> + <has_line line="processing p-Toluenesulfonamide " /> + <has_line line="processing Rifaximin " /> + <has_line line="processing Spinosad A (Spinosyn A) " /> + <has_line line="processing TCMTB " /> + <has_line line="processing Trichlorfon (Dylox) " /> + <has_line line="processing Tylosin " /> + <has_line line=" non detected in precursor file " min="6" /> + </xml> + + <xml name="has_not_debug_stdout"> + <has_line negate="true" line=" acquisitionNum mz68 mz71 mz74 mz81 mz82 mz83" /> + <has_line negate="true" line=" acquisitionNum mz67 mz71 mz84 mz85 mz86 mz87" /> + <has_line negate="true" line=" mz243 mz248 mz256 mz257 mz258" /> + </xml> + + <xml name="has_debug_stdout"> + <has_line line=" acquisitionNum mz68 mz71 mz74 mz81 mz82 mz83" /> + <has_line line=" acquisitionNum mz67 mz71 mz84 mz85 mz86 mz87" /> + <!-- + <has_line line=" acquisitionNum mz63 mz67 mz71 mz73 mz77 mz79" /> + <has_line line=" acquisitionNum mz79 mz81 mz84 mz86 mz88 mz90" /> + <has_line line=" acquisitionNum mz67 mz69 mz71 mz72 mz73 mz75" /> + <has_line line=" acquisitionNum mz99 mz100 mz109 mz132 mz135 mz142 mz145" /> + <has_line line=" acquisitionNum mz105 mz109 mz111 mz112 mz114 mz115" /> + <has_line line=" acquisitionNum mz105 mz109 mz111 mz116 mz119 mz125" /> + <has_line line=" acquisitionNum mz79 mz91 mz92 mz94 mz103 mz104" /> + <has_line line=" acquisitionNum mz61 mz73 mz76 mz79 mz91 mz92" /> + <has_line line=" acquisitionNum mz67 mz72 mz73 mz76 mz77 mz78" /> + <has_line line=" acquisitionNum mz123 mz124 mz125 mz127 mz130 mz131" /> + <has_line line=" acquisitionNum mz96 mz97 mz99 mz100 mz101 mz103" /> + <has_line line=" acquisitionNum mz69 mz72 mz73 mz79 mz81 mz85" /> + <has_line line=" acquisitionNum mz82 mz83 mz85 mz87 mz91 mz94" /> + <has_line line=" acquisitionNum mz60 mz68 mz69 mz71 mz78 mz81" /> + <has_line line=" acquisitionNum mz84 mz86 mz87 mz88 mz89 mz91" /> + <has_line line=" acquisitionNum mz86 mz95 mz97 mz105 mz106 mz107" /> + <has_line line=" acquisitionNum mz72 mz91 mz99 mz100 mz105 mz109" /> + <has_line line=" acquisitionNum mz216 mz225 mz229 mz245 mz247 mz249" /> + <has_line line=" acquisitionNum mz61 mz70 mz71 mz72 mz77 mz81" /> + <has_line line=" acquisitionNum mz112 mz121 mz133 mz134 mz135 mz136" /> + <has_line line=" acquisitionNum mz115 mz116 mz119 mz120 mz127 mz135" /> + <has_line line=" acquisitionNum mz86 mz90 mz91 mz94 mz99 mz100" /> + <has_line line=" acquisitionNum mz219 mz221 mz223 mz225 mz226 mz227" /> + <has_line line=" acquisitionNum mz230 mz233 mz241 mz243 mz255 mz260" /> + <has_line line=" acquisitionNum mz75 mz81 mz89 mz91 mz93 mz95" /> + <has_line line=" acquisitionNum mz69 mz72 mz75 mz80 mz81 mz83" /> + <has_line line=" acquisitionNum mz77 mz79 mz81 mz82 mz83 mz85" /> + --> + <has_line line=" mz243 mz248 mz256 mz257 mz258" /> + </xml> + + <xml name="has_not_verbose_stdout"> + <has_line negate="true" line=" fragments : 68 71 74 81 82 83 84 94 97 99 102 103 104 105 109 111 112 117 118 120 121 123 124 126 128 134 136 137 139 140 141 144 146 147 148 149 150 151 152 154 162 163 164 165 166 167 168 180 181 182 183" /> + <has_line negate="true" line=" fragments : 67 71 84 85 86 87 88 89 91 92 95 96 98 99 105 107 110 112 114 116 118 119 120 123 124 126 127 128 129 130 132 134 135 136 139 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/compounds_pos.csv Wed Jun 22 13:07:01 2022 +0000 @@ -0,0 +1,33 @@ +Compounds,mz,rt +2-diethylamino-6-methyl pyrimidin-4-ol one,182.12879,345.0 +5-hydroxy-thiabendazole,218.03826,315.0 +acetamiprid-N-desmethyl,209.05885,526.2 +Acetochlor,270.12554,1158.6 +Avermectin B1a (Abamectin),895.49221,1663.8 +Benzophenone-3 (Oxybenzone),229.08592,1178.4 +Butocarboxim,191.0849,1267.8 +Carbendazim,192.07676,339.0 +Cefoperazone,646.1497,1755.0 +Chlorfenvinphos,358.97681,1255.8 +Chlormequat,122.0737,54.0 +Desisopropylatrazine,174.0541,399.0 +Dichlorvos,220.9532,763.2 +Dimethyldithiophosphate,158.96979,615.0 +Emamectin B1a,886.5311,1663.8 +Fluopyram,397.05369,1161.0 +Hydroxy-tebuconazole,324.14733,1098.6 +Isoproturon,207.14919,936.0 +Ivermectin B1a ,897.4971,1650.0 +Malathion dicarboxilic acid,274.98075,574.8 +Methamidophos,142.0086,139.2 +Metolachlor,284.14119,1158.0 +"N,N-diethyl-m-toluamide ou DEET",192.13829,945.0 +Nigericin,747.4654,1663.8 +Omethoate,214.02975,237.0 +Prochloraz,376.03809,1271.4 +p-Toluenesulfonamide,172.04323,393.0 +Rifaximin,786.3596,1183.2 +Spinosad A (Spinosyn A),732.4681,1212.0 +TCMTB,238.9766,1032.0 +Trichlorfon (Dylox),256.9299,444.0 +Tylosin,916.5264,909.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/peaklist_precursors.csv Wed Jun 22 13:07:01 2022 +0000 @@ -0,0 +1,2737 @@ +"grpid","mz","mzmin","mzmax","rt","rtmin","rtmax","into","intb","maxo","sn","sample","cid","filename","rtminCorrected","rtmaxCorrected","inPurity","pid","precurMtchID","precurMtchScan","precurMtchRT","precurMtchMZ","precurMtchPPM","retentionTime","fileid","seqNum","purity_pass_flag" +"674",121.993879318102,121.993766784668,121.99397277832,69.4840944720271,63.56629999998,78.89839999998,3933750.80009461,3933736.08127861,395685,395684,3,16484,"HBMSPE21_024.mzML",62.750400858841,78.0434285273669,0.526099609140227,6641,218,217,64.8261,121.993896484375,0.140714213529811,65.2467,3,218,TRUE 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+"1974",173.961007885901,173.960876464844,173.961135864258,253.560897315001,242.41150000002,265.7295,54378624.046895,53929620.6511686,2357849.25,256,1,3292,"HBMSPE21_026.mzML",241.131250454048,264.424437419758,0.945843487697185,207,620,619,265.7295,173.9609375,0.404607342812583,266.08699999998,1,620,TRUE +"1991",174.054129429069,174.053955078125,174.054290771484,397.77084297831,392.65999999998,409.5312,16307777.1031281,16298470.0580809,3203289.75,1533,1,932,"HBMSPE21_026.mzML",391.249869702803,408.11093443942,0.568399909394457,546,1132,1131,396.6774,174.054122924805,0.0373692021664848,397.11790000002,1,1132,TRUE +"1991",174.054129429069,174.053955078125,174.054290771484,397.77084297831,392.65999999998,409.5312,16307777.1031281,16298470.0580809,3203289.75,1533,1,932,"HBMSPE21_026.mzML",391.249869702803,408.11093443942,0.636840647697994,547,1134,1133,397.31779999998,174.054046630859,0.47570379131274,397.74139999998,1,1134,TRUE 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+"1991",174.054129429069,174.053955078125,174.054290771484,397.77084297831,392.65999999998,409.5312,16307777.1031281,16298470.0580809,3203289.75,1533,1,932,"HBMSPE21_026.mzML",391.249869702803,408.11093443942,0.651767258635252,551,1142,1141,399.81559999998,174.054077148438,0.300369955654238,400.25050000002,1,1142,TRUE +"1991",174.054129429069,174.053955078125,174.054290771484,397.77084297831,392.65999999998,409.5312,16307777.1031281,16298470.0580809,3203289.75,1533,1,932,"HBMSPE21_026.mzML",391.249869702803,408.11093443942,0.610232440170788,552,1144,1143,400.44070000002,174.054122924805,0.0373692021664848,400.8792,1,1144,TRUE +"1991",174.054129429069,174.053955078125,174.054290771484,397.77084297831,392.65999999998,409.5312,16307777.1031281,16298470.0580809,3203289.75,1533,1,932,"HBMSPE21_026.mzML",391.249869702803,408.11093443942,0.533561865982376,553,1146,1145,401.07919999998,174.054260253906,0.751633058296775,401.50720000002,1,1146,TRUE 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