From 811f290e6b988dae9ad2d510b1caaa6747effafb Mon Sep 17 00:00:00 2001 From: DamienCode404 Date: Fri, 11 Oct 2024 15:36:59 +0200 Subject: [PATCH] Add camera new tools --- tools/camera/.shed.yml | 49 +++++++++++++++++-- tools/camera/CAMERA_findAdducts.R | 1 + tools/camera/CAMERA_findIsotopes.R | 1 + tools/camera/CAMERA_groupCorr.R | 1 + tools/camera/CAMERA_groupFWHM.R | 1 + tools/camera/findAdducts.xml | 1 + tools/camera/findIsotopes.xml | 1 + tools/camera/groupCorr.xml | 1 + tools/camera/groupFWHM.xml | 1 + tools/camera/static/images/findAdducts.png | 1 + tools/camera/static/images/findIsotopes.png | 1 + tools/camera/static/images/groupCorr.png | 1 + tools/camera/static/images/groupFWHM.png | 1 + tools/camera/test-data/13_faahKO.zip | 1 + tools/camera/test-data/faahKO | 1 + ...erged.groupChromPeaks.fillChromPeaks.RData | 1 + ...mPeaks.fillChromPeaks.fwhm.groupCorr.RData | 1 + ...romPeaks.fwhm.groupCorr.findIsotopes.RData | 1 + ...m.groupCorr.findIsotopes.findAdducts.RData | 1 + ...s.findAdducts.variableMetadata.tsv.tabular | 1 + ....findIsotopes.variableMetadata.tsv.tabular | 1 + ...whm.groupCorr.variableMetadata.tsv.tabular | 1 + ....groupChromPeaks.fillChromPeaks.fwhm.rdata | 1 + ...s.fillChromPeaks.fwhm.variableMetadata.tsv | 1 + 24 files changed, 68 insertions(+), 4 deletions(-) create mode 120000 tools/camera/CAMERA_findAdducts.R create mode 120000 tools/camera/CAMERA_findIsotopes.R create mode 120000 tools/camera/CAMERA_groupCorr.R create mode 120000 tools/camera/CAMERA_groupFWHM.R create mode 120000 tools/camera/findAdducts.xml create mode 120000 tools/camera/findIsotopes.xml create mode 120000 tools/camera/groupCorr.xml create mode 120000 tools/camera/groupFWHM.xml create mode 120000 tools/camera/static/images/findAdducts.png create mode 120000 tools/camera/static/images/findIsotopes.png create mode 120000 tools/camera/static/images/groupCorr.png create mode 120000 tools/camera/static/images/groupFWHM.png create mode 120000 tools/camera/test-data/13_faahKO.zip create mode 120000 tools/camera/test-data/faahKO create mode 120000 tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.RData create mode 120000 tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData create mode 120000 tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData create mode 120000 tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData create mode 120000 tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv.tabular create mode 120000 tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.variableMetadata.tsv.tabular create mode 120000 tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.variableMetadata.tsv.tabular create mode 120000 tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.rdata create mode 120000 tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.variableMetadata.tsv diff --git a/tools/camera/.shed.yml b/tools/camera/.shed.yml index 1804c3d66..1932de3ae 100644 --- a/tools/camera/.shed.yml +++ b/tools/camera/.shed.yml @@ -7,8 +7,8 @@ definitions: name: camera owner: workflow4metabolomics -remote_repository_url: -homepage_url: +remote_repository_url: +homepage_url: categories: - Metabolomics @@ -41,10 +41,51 @@ repositories: owner: workflow4metabolomics include: [*default-includes, abims_CAMERA_combinexsAnnos.xml, CAMERA_combinexsAnnos.r] + camera_groupfwhm: + description: '[Metabolomics][W4M][LC-MS] CAMERA R Package - Peak Grouping by Full Width at Half Maximum (FWHM)' + long_description: | + Group peaks within a defined retention time window using Full Width at Half Maximum (FWHM). + Facilitates the detection of chromatographic features across different samples for LC-MS data. + Part of the W4M project: http://workflow4metabolomics.org + CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html + owner: workflow4metabolomics + include: + [*default-includes, camera_groupfwhm.xml, camera_groupfwhm.r] + camera_groupcorr: + description: '[Metabolomics][W4M][LC-MS] CAMERA R Package - Peak Grouping by Correlation' + long_description: | + Group peaks based on their retention time and intensity correlations across samples, + identifying peaks likely to originate from the same compound. This helps enhance feature annotation + and identification in LC-MS data. + Part of the W4M project: http://workflow4metabolomics.org + CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html + owner: workflow4metabolomics + include: + [*default-includes, groupCorr.xml, CAMERA_groupCorr.R] + camera_findisotopes: + description: '[Metabolomics][W4M][LC-MS] CAMERA R Package - Isotope Detection' + long_description: | + Detect isotope patterns in LC-MS peak lists based on mass differences and expected isotope ratios, + annotating isotopes for use in downstream metabolomic analysis. + Part of the W4M project: http://workflow4metabolomics.org + CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html + owner: workflow4metabolomics + include: + [*default-includes, findIsotopes.xml, CAMERA_findIsotopes.R] + camera_findadducts: + description: '[Metabolomics][W4M][LC-MS] CAMERA R Package - Adduct Detection' + long_description: | + Identify possible adducts in mass spectrometry data by detecting characteristic mass shifts between peaks, + facilitating the determination of molecular ions and their adducts for more accurate metabolite identification. + Part of the W4M project: http://workflow4metabolomics.org + CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html + owner: workflow4metabolomics + include: + [*default-includes, findAdducts.xml, CAMERA_findAdducts.R] suite: name: suite_camera - owner: lecorguille + owner: workflow4metabolomics homepage_url: http://workflow4metabolomics.org description: '[Metabolomics][W4M][LC-MS] CAMERA R Package - Annotation - Collection of annotation related methods for mass spectrometry data' long_description: | @@ -52,4 +93,4 @@ suite: isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments Part of the W4M project: http://workflow4metabolomics.org - CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html \ No newline at end of file + CAMERA: http://bioconductor.org/packages/release/bioc/html/CAMERA.html diff --git a/tools/camera/CAMERA_findAdducts.R b/tools/camera/CAMERA_findAdducts.R new file mode 120000 index 000000000..a622c0cb8 --- /dev/null +++ b/tools/camera/CAMERA_findAdducts.R @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/CAMERA_findAdducts.R \ No newline at end of file diff --git a/tools/camera/CAMERA_findIsotopes.R b/tools/camera/CAMERA_findIsotopes.R new file mode 120000 index 000000000..c61ced4f5 --- /dev/null +++ b/tools/camera/CAMERA_findIsotopes.R @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/CAMERA_findIsotopes.R \ No newline at end of file diff --git a/tools/camera/CAMERA_groupCorr.R b/tools/camera/CAMERA_groupCorr.R new file mode 120000 index 000000000..919590446 --- /dev/null +++ b/tools/camera/CAMERA_groupCorr.R @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/CAMERA_groupCorr.R \ No newline at end of file diff --git a/tools/camera/CAMERA_groupFWHM.R b/tools/camera/CAMERA_groupFWHM.R new file mode 120000 index 000000000..447390916 --- /dev/null +++ b/tools/camera/CAMERA_groupFWHM.R @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/CAMERA_groupFWHM.R \ No newline at end of file diff --git a/tools/camera/findAdducts.xml b/tools/camera/findAdducts.xml new file mode 120000 index 000000000..1ba4f305a --- /dev/null +++ b/tools/camera/findAdducts.xml @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/findAdducts.xml \ No newline at end of file diff --git a/tools/camera/findIsotopes.xml b/tools/camera/findIsotopes.xml new file mode 120000 index 000000000..ec27f661a --- /dev/null +++ b/tools/camera/findIsotopes.xml @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/findIsotopes.xml \ No newline at end of file diff --git a/tools/camera/groupCorr.xml b/tools/camera/groupCorr.xml new file mode 120000 index 000000000..c472edc6b --- /dev/null +++ b/tools/camera/groupCorr.xml @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/groupCorr.xml \ No newline at end of file diff --git a/tools/camera/groupFWHM.xml b/tools/camera/groupFWHM.xml new file mode 120000 index 000000000..5a42e47ef --- /dev/null +++ b/tools/camera/groupFWHM.xml @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/groupFWHM.xml \ No newline at end of file diff --git a/tools/camera/static/images/findAdducts.png b/tools/camera/static/images/findAdducts.png new file mode 120000 index 000000000..4b679a423 --- /dev/null +++ b/tools/camera/static/images/findAdducts.png @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/static/images/findAdducts.png \ No newline at end of file diff --git a/tools/camera/static/images/findIsotopes.png b/tools/camera/static/images/findIsotopes.png new file mode 120000 index 000000000..0b82bf617 --- /dev/null +++ b/tools/camera/static/images/findIsotopes.png @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/static/images/findIsotopes.png \ No newline at end of file diff --git a/tools/camera/static/images/groupCorr.png b/tools/camera/static/images/groupCorr.png new file mode 120000 index 000000000..35a7d8d7f --- /dev/null +++ b/tools/camera/static/images/groupCorr.png @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/static/images/groupCorr.png \ No newline at end of file diff --git a/tools/camera/static/images/groupFWHM.png b/tools/camera/static/images/groupFWHM.png new file mode 120000 index 000000000..0999135e2 --- /dev/null +++ b/tools/camera/static/images/groupFWHM.png @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/static/images/groupFWHM.png \ No newline at end of file diff --git a/tools/camera/test-data/13_faahKO.zip b/tools/camera/test-data/13_faahKO.zip new file mode 120000 index 000000000..ef2a9f9eb --- /dev/null +++ b/tools/camera/test-data/13_faahKO.zip @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/13_faahKO.zip \ No newline at end of file diff --git a/tools/camera/test-data/faahKO b/tools/camera/test-data/faahKO new file mode 120000 index 000000000..82b4ce47b --- /dev/null +++ b/tools/camera/test-data/faahKO @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/faahKO \ No newline at end of file diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.RData b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.RData new file mode 120000 index 000000000..63e2163fb --- /dev/null +++ b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.RData @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/xset.merged.groupChromPeaks.fillChromPeaks.RData \ No newline at end of file diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData new file mode 120000 index 000000000..035596d42 --- /dev/null +++ b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.RData \ No newline at end of file diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData new file mode 120000 index 000000000..3237e20a1 --- /dev/null +++ b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.RData \ No newline at end of file diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData new file mode 120000 index 000000000..c3f70ce3a --- /dev/null +++ b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData \ No newline at end of file diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv.tabular b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv.tabular new file mode 120000 index 000000000..e94493a17 --- /dev/null +++ b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv.tabular @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv.tabular \ No newline at end of file diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.variableMetadata.tsv.tabular b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.variableMetadata.tsv.tabular new file mode 120000 index 000000000..4ac73076e --- /dev/null +++ b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.variableMetadata.tsv.tabular @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.findIsotopes.variableMetadata.tsv.tabular \ No newline at end of file diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.variableMetadata.tsv.tabular b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.variableMetadata.tsv.tabular new file mode 120000 index 000000000..6c19fc55c --- /dev/null +++ b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.variableMetadata.tsv.tabular @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.groupCorr.variableMetadata.tsv.tabular \ No newline at end of file diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.rdata b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.rdata new file mode 120000 index 000000000..bf43220b5 --- /dev/null +++ b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.rdata @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.rdata \ No newline at end of file diff --git a/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.variableMetadata.tsv b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.variableMetadata.tsv new file mode 120000 index 000000000..2834a676c --- /dev/null +++ b/tools/camera/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.variableMetadata.tsv @@ -0,0 +1 @@ +/home/laberca/galaxy/tools/SUITE_CAMERA/test-data/xset.merged.groupChromPeaks.fillChromPeaks.fwhm.variableMetadata.tsv \ No newline at end of file