| Previous changeset 2:75dafb766417 (2022-06-29) Next changeset 4:050cfef6ba65 (2023-06-15) |
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Commit message:
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8714723083359049eb1a715a946851e07f8a3a20 |
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modified:
ramclustr.xml ramclustr_wrapper.R test-data/test1_spec_abundance_xcms_1.csv test-data/test2_spec_abundance_xcms_2.csv test-data/test3_spec_abundance_csv_1.csv |
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| diff -r 75dafb766417 -r 2ec9253a647e ramclustr.xml --- a/ramclustr.xml Wed Jun 29 10:00:10 2022 +0000 +++ b/ramclustr.xml Tue Sep 20 14:43:56 2022 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy1"> +<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2"> <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description> <macros> <import>macros.xml</import> @@ -129,7 +129,7 @@ <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" /> </section> </section> - <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/> + <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="20"/> <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/> </test> <test><!-- TEST 3 --> |
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| diff -r 75dafb766417 -r 2ec9253a647e ramclustr_wrapper.R --- a/ramclustr_wrapper.R Wed Jun 29 10:00:10 2022 +0000 +++ b/ramclustr_wrapper.R Tue Sep 20 14:43:56 2022 +0000 |
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| @@ -1,10 +1,9 @@ -store_output <- function( - ramclustr_obj, - output_merge_msp, - output_spec_abundance, - msp_file) { +store_output <- function(ramclustr_obj, + output_merge_msp, + output_spec_abundance, + msp_file) { RAMClustR::write.msp(ramclustr_obj, one.file = output_merge_msp) - write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE) + write.csv(ramclustr_obj$SpecAbund, file = output_spec_abundance, row.names = TRUE, quote = FALSE) if (!is.null(msp_file)) { exp_name <- ramclustr_obj$ExpDes[[1]][which(row.names(ramclustr_obj$ExpDes[[1]]) == "Experiment"), 1] @@ -36,27 +35,25 @@ return(data) } -ramclustr_xcms <- function( - input_xcms, - use_pheno, - sr, - st = NULL, - cor_method, - maxt, - linkage, - min_module_size, - hmax, - deep_split, - normalize, - metadata_file = NULL, - qc_inj_range, - block_size, - mult, - mzdec, - rt_only_low_n, - replace_zeros, - exp_design = NULL -) { +ramclustr_xcms <- function(input_xcms, + use_pheno, + sr, + st = NULL, + cor_method, + maxt, + linkage, + min_module_size, + hmax, + deep_split, + normalize, + metadata_file = NULL, + qc_inj_range, + block_size, + mult, + mzdec, + rt_only_low_n, + replace_zeros, + exp_design = NULL) { obj <- load(input_xcms) batch <- NULL @@ -100,33 +97,32 @@ order = order, qc = qc, ExpDes = experiment - ) + ) return(x) } -ramclustr_csv <- function( - ms, - idmsms, - sr, - st, - cor_method, - maxt, - linkage, - min_module_size, - hmax, - deep_split, - normalize, - metadata_file = NULL, - qc_inj_range, - block_size, - mult, - mzdec, - rt_only_low_n, - replace_zeros, - exp_design = NULL -) { - if (!file.exists(idmsms)) +ramclustr_csv <- function(ms, + idmsms, + sr, + st, + cor_method, + maxt, + linkage, + min_module_size, + hmax, + deep_split, + normalize, + metadata_file = NULL, + qc_inj_range, + block_size, + mult, + mzdec, + rt_only_low_n, + replace_zeros, + exp_design = NULL) { + if (!file.exists(idmsms)) { idmsms <- NULL + } batch <- NULL order <- NULL @@ -169,6 +165,6 @@ order = order, qc = qc, ExpDes = experiment - ) - return(x) + ) + return(x) } |
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| diff -r 75dafb766417 -r 2ec9253a647e test-data/test1_spec_abundance_xcms_1.csv --- a/test-data/test1_spec_abundance_xcms_1.csv Wed Jun 29 10:00:10 2022 +0000 +++ b/test-data/test1_spec_abundance_xcms_1.csv Tue Sep 20 14:43:56 2022 +0000 |
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| b'@@ -1,21 +1,21 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| diff -r 75dafb766417 -r 2ec9253a647e test-data/test2_spec_abundance_xcms_2.csv --- a/test-data/test2_spec_abundance_xcms_2.csv Wed Jun 29 10:00:10 2022 +0000 +++ b/test-data/test2_spec_abundance_xcms_2.csv Tue Sep 20 14:43:56 2022 +0000 |
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| b |
| diff -r 75dafb766417 -r 2ec9253a647e test-data/test3_spec_abundance_csv_1.csv --- a/test-data/test3_spec_abundance_csv_1.csv Wed Jun 29 10:00:10 2022 +0000 +++ b/test-data/test3_spec_abundance_csv_1.csv Tue Sep 20 14:43:56 2022 +0000 |
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