From 2369936d49c6e21702626b100ea81579651b0889 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 2 Jan 2025 10:01:57 +0100 Subject: [PATCH 1/5] add required files for pulsar closes #279 --- tools/xcms/msnbase_readmsdata.xml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tools/xcms/msnbase_readmsdata.xml b/tools/xcms/msnbase_readmsdata.xml index 1c4fa5fae..ca03b6bd2 100644 --- a/tools/xcms/msnbase_readmsdata.xml +++ b/tools/xcms/msnbase_readmsdata.xml @@ -7,6 +7,10 @@ + + + + Date: Thu, 2 Jan 2025 10:03:51 +0100 Subject: [PATCH 2/5] bump version --- tools/xcms/msnbase_readmsdata.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/xcms/msnbase_readmsdata.xml b/tools/xcms/msnbase_readmsdata.xml index ca03b6bd2..fb7ebdc68 100644 --- a/tools/xcms/msnbase_readmsdata.xml +++ b/tools/xcms/msnbase_readmsdata.xml @@ -1,4 +1,4 @@ - + Imports mass-spectrometry data files From 9659d2c25b7db41f29a98a1857fdd78bab4067b2 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Wed, 8 Jan 2025 12:04:21 +0100 Subject: [PATCH 3/5] include missing required files for the rest of the tools in repo --- .../abims_CAMERA_annotateDiffreport.xml | 4 + tools/camera/abims_CAMERA_combinexsAnnos.xml | 4 + tools/camera/macros.xml | 2 +- .../abims_correlation_analysis.xml | 5 +- tools/ipo/ipo4retgroup.xml | 7 +- tools/ipo/ipo4xcmsSet.xml | 6 +- .../kmd_hmdb_data_plot/kmd_hmdb_data_plot.xml | 6 +- tools/mixmodel4repeated_measures/mixmodel.xml | 15 +- tools/ms2snoop/MS2snoop.xml | 5 +- tools/ms2snoop/macros.xml | 16 +- tools/mzxmlshaper/mzXMLShaper.xml | 15 +- tools/nmr_annotation/asics_xml.xml | 7 +- .../nmr_annotation2d/annotationRmn2D_xml.xml | 15 +- .../NmrPreprocessing_xml.xml | 7 +- tools/nmr_preprocessing/ReadFids_xml.xml | 7 +- tools/normalization/NmrNormalization_xml.xml | 7 +- tools/w4mconcatenate/concat.xml | 169 +++++++++--------- tools/xcms/abims_xcms_fillPeaks.xml | 4 + tools/xcms/abims_xcms_group.xml | 4 + tools/xcms/abims_xcms_refine.xml | 5 +- tools/xcms/abims_xcms_retcor.xml | 4 + tools/xcms/abims_xcms_summary.xml | 5 +- tools/xcms/abims_xcms_xcmsSet.xml | 4 + tools/xcms/macros_xcms.xml | 2 +- tools/xcms/xcms_export_samplemetadata.xml | 4 + tools/xcms/xcms_merge.xml | 4 + tools/xcms/xcms_plot_chromatogram.xml | 4 + 27 files changed, 220 insertions(+), 117 deletions(-) diff --git a/tools/camera/abims_CAMERA_annotateDiffreport.xml b/tools/camera/abims_CAMERA_annotateDiffreport.xml index dd328e110..02d34ad4c 100644 --- a/tools/camera/abims_CAMERA_annotateDiffreport.xml +++ b/tools/camera/abims_CAMERA_annotateDiffreport.xml @@ -7,6 +7,10 @@ + + + + + + + + 1.48.0 - 1 + 2 r-snow diff --git a/tools/correlation_analysis/abims_correlation_analysis.xml b/tools/correlation_analysis/abims_correlation_analysis.xml index 1c01862fa..1a42d5b22 100644 --- a/tools/correlation_analysis/abims_correlation_analysis.xml +++ b/tools/correlation_analysis/abims_correlation_analysis.xml @@ -1,4 +1,4 @@ - + to highlight ion correlations considering PC-groups @@ -7,6 +7,9 @@ r-reshape r-mass + + + Rscript '$__tool_directory__/correlation_analysis.r' diff --git a/tools/ipo/ipo4retgroup.xml b/tools/ipo/ipo4retgroup.xml index 2f2e2d706..05bc92044 100644 --- a/tools/ipo/ipo4retgroup.xml +++ b/tools/ipo/ipo4retgroup.xml @@ -1,4 +1,4 @@ - + IPO optimization process for xcms.groupChromPeaks and xcms.adjustRtime @@ -7,7 +7,10 @@ - + + + + + IPO optimization process for xcms.findChromPeaks @@ -7,6 +7,10 @@ + + + + macro.xml 1.0.0 - 0 + 1 topic_0091 @@ -19,6 +19,10 @@ plotly kmd_hmdb_api_client + + + + + ANOVA for repeated measures statistics @@ -8,6 +8,11 @@ r-gridExtra bioconductor-multtest + + + + + sirius-csifingerid zip + + + @@ -310,7 +313,7 @@ Description MS2snoop use results of msPurity to find spectra of standards listed in a compounds file. Check the fragments and precursor using correlation of -among the different scans of fragments +among the different scans of fragments ----------------- Workflow position diff --git a/tools/ms2snoop/macros.xml b/tools/ms2snoop/macros.xml index af8fb25af..2c95924c4 100644 --- a/tools/ms2snoop/macros.xml +++ b/tools/ms2snoop/macros.xml @@ -26,13 +26,13 @@ msPurity.frag4feature Compounds file | A tabulated, comma or semicolon separated values file whith compounds. Its format is as follow: - | + | | At least 4 columns: | **compound_name**: The name of the compound | **mz**: The m/z ratio | **rtsec**: The retention time in seconds | **inchikey**: The compound's inchi key - | + | | An optional column can be added: | **elemcomposition**: The elemental composition of the molecule @@ -66,10 +66,10 @@ compound_fragments_result.tsv | tabular output | Array with p rows (corresponding to the fragments for the different compounds of the compounds file) - | Last column "corvalid" is a boolean for validated fragments + | Last column "corvalid" is a boolean for validated fragments processing_file.pdf - | pdf output + | pdf output | For each compound of the compounds file, Graph of the all fragments with parents (or most intense peak if parent is not detected in the fragments. At the end the pdf file a graph of the spectra with @@ -103,7 +103,7 @@ Changelog/News mzref and the rtref to be the 1st, the 2nd and the 3rd columns respectively, and the header was somewhat ignored in the compound file. - | + | | Now, we'd like to add some new columns, some of them are optional. This new format of file implies a better definition of the columns order, @@ -114,7 +114,7 @@ Changelog/News | - **elemcomposition** [OPTIONAL] ; | - **mz** [MANDATORY] ; | - **rtsec** [MANDATORY]. - | + | | These names can be written indiferentially in lower and/or upper case. The new definition being incompatible with the older one, that was more flexible, but also more error-prone. @@ -139,7 +139,7 @@ Changelog/News 2.2.1 - 0 + 1 @@ -236,4 +236,4 @@ Changelog/News - \ No newline at end of file + diff --git a/tools/mzxmlshaper/mzXMLShaper.xml b/tools/mzxmlshaper/mzXMLShaper.xml index c58fa14b9..340976a3b 100644 --- a/tools/mzxmlshaper/mzXMLShaper.xml +++ b/tools/mzxmlshaper/mzXMLShaper.xml @@ -1,4 +1,4 @@ - + conversion into XCMS-supported mz(X)ML file formats @@ -8,6 +8,9 @@ bioconductor-mzr r-w4mrutils + + + 10.18129/B9.bioc.mzR - \ No newline at end of file + diff --git a/tools/nmr_annotation/asics_xml.xml b/tools/nmr_annotation/asics_xml.xml index c044f5f87..a1bf1a9db 100644 --- a/tools/nmr_annotation/asics_xml.xml +++ b/tools/nmr_annotation/asics_xml.xml @@ -1,4 +1,4 @@ - + Annotation of complex mixture NMR spectra and metabolite proportion estimation @@ -6,6 +6,11 @@ r-batch r-asics + + + + + diff --git a/tools/nmr_annotation2d/annotationRmn2D_xml.xml b/tools/nmr_annotation2d/annotationRmn2D_xml.xml index 56db47aed..ba7fb7b82 100644 --- a/tools/nmr_annotation2d/annotationRmn2D_xml.xml +++ b/tools/nmr_annotation2d/annotationRmn2D_xml.xml @@ -1,4 +1,4 @@ - + Annotation of complex mixture bidimensional NMR spectra @@ -13,7 +13,18 @@ r-jsonlite r-stringi - + + + + + + + + + + + + diff --git a/tools/nmr_preprocessing/NmrPreprocessing_xml.xml b/tools/nmr_preprocessing/NmrPreprocessing_xml.xml index 5671c7448..bb994dc6e 100644 --- a/tools/nmr_preprocessing/NmrPreprocessing_xml.xml +++ b/tools/nmr_preprocessing/NmrPreprocessing_xml.xml @@ -1,4 +1,4 @@ - + Preprocessing of 1D NMR spectra @@ -9,6 +9,11 @@ r-ptw r-matrix + + + + + diff --git a/tools/nmr_preprocessing/ReadFids_xml.xml b/tools/nmr_preprocessing/ReadFids_xml.xml index 86bbfc082..e5d5448fa 100644 --- a/tools/nmr_preprocessing/ReadFids_xml.xml +++ b/tools/nmr_preprocessing/ReadFids_xml.xml @@ -1,4 +1,4 @@ - + Read Bruker NMR raw files @@ -6,6 +6,11 @@ + + + + + diff --git a/tools/normalization/NmrNormalization_xml.xml b/tools/normalization/NmrNormalization_xml.xml index 45cb84d91..766dab734 100644 --- a/tools/normalization/NmrNormalization_xml.xml +++ b/tools/normalization/NmrNormalization_xml.xml @@ -1,10 +1,15 @@ - + Normalization of (preprocessed) spectra r-batch + + + + + diff --git a/tools/w4mconcatenate/concat.xml b/tools/w4mconcatenate/concat.xml index aa74348dd..7c5df0019 100644 --- a/tools/w4mconcatenate/concat.xml +++ b/tools/w4mconcatenate/concat.xml @@ -1,31 +1,36 @@ - + to merge two metadata tables r-base r-dplyr r-w4mrutils + + + + + - - + + - + - + - + - + @@ -73,22 +78,22 @@ - + - + - - - + + + - + - + - + @@ -99,14 +104,14 @@ - + - - + + - + @@ -116,51 +121,51 @@ - + - + - + 10.1093/bioinformatics/btu813 - + - + - \ No newline at end of file + diff --git a/tools/xcms/abims_xcms_fillPeaks.xml b/tools/xcms/abims_xcms_fillPeaks.xml index d224550a0..fbd39043d 100644 --- a/tools/xcms/abims_xcms_fillPeaks.xml +++ b/tools/xcms/abims_xcms_fillPeaks.xml @@ -8,6 +8,10 @@ + + + + + + + + - + + + + + + + + bioconductor-camera r-batch - + + + + + + + + 3.12.0 - 1 + 2 21.09 diff --git a/tools/xcms/xcms_export_samplemetadata.xml b/tools/xcms/xcms_export_samplemetadata.xml index f1e69a47c..eccd0802d 100644 --- a/tools/xcms/xcms_export_samplemetadata.xml +++ b/tools/xcms/xcms_export_samplemetadata.xml @@ -7,6 +7,10 @@ + + + + + + + + macros_xcms.xml + + + + Date: Wed, 8 Jan 2025 12:06:40 +0100 Subject: [PATCH 4/5] include missing requirement for click in a version roughly from the same timeline --- tools/kmd_hmdb_data_plot/kmd_hmdb_data_plot.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/kmd_hmdb_data_plot/kmd_hmdb_data_plot.xml b/tools/kmd_hmdb_data_plot/kmd_hmdb_data_plot.xml index 41559c7bd..020cc1c63 100644 --- a/tools/kmd_hmdb_data_plot/kmd_hmdb_data_plot.xml +++ b/tools/kmd_hmdb_data_plot/kmd_hmdb_data_plot.xml @@ -14,6 +14,7 @@ operation_3803 + click python pandas plotly From e046d1ff8bd6ba618357133d36e7486412b734e2 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Wed, 8 Jan 2025 12:09:32 +0100 Subject: [PATCH 5/5] fix double and triple slashes slesh is already part of the macro, not sure if this can faiil sometimes, but this commit should be correct always --- tools/camera/abims_CAMERA_annotateDiffreport.xml | 2 +- tools/camera/abims_CAMERA_combinexsAnnos.xml | 2 +- tools/xcms/abims_xcms_fillPeaks.xml | 2 +- tools/xcms/abims_xcms_group.xml | 2 +- tools/xcms/abims_xcms_refine.xml | 2 +- tools/xcms/abims_xcms_retcor.xml | 2 +- tools/xcms/abims_xcms_summary.xml | 2 +- tools/xcms/abims_xcms_xcmsSet.xml | 2 +- tools/xcms/msnbase_readmsdata.xml | 2 +- tools/xcms/xcms_export_samplemetadata.xml | 2 +- tools/xcms/xcms_merge.xml | 2 +- tools/xcms/xcms_plot_chromatogram.xml | 2 +- 12 files changed, 12 insertions(+), 12 deletions(-) diff --git a/tools/camera/abims_CAMERA_annotateDiffreport.xml b/tools/camera/abims_CAMERA_annotateDiffreport.xml index 02d34ad4c..17d5cb164 100644 --- a/tools/camera/abims_CAMERA_annotateDiffreport.xml +++ b/tools/camera/abims_CAMERA_annotateDiffreport.xml @@ -14,7 +14,7 @@ diff --git a/tools/xcms/xcms_merge.xml b/tools/xcms/xcms_merge.xml index 97ff8443e..2797ef412 100644 --- a/tools/xcms/xcms_merge.xml +++ b/tools/xcms/xcms_merge.xml @@ -14,7 +14,7 @@