mv metams in tools folder

workflow4metabolomics · Oct 9, 2024 · d3b6bd2 · d3b6bd2
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diff --git a/metams/macros/macros.xml → tools/metams/macros/macros.xml b/metams/macros/macros.xml → tools/metams/macros/macros.xml
diff --git a/metams/metaMS_plot/.shed.yml → tools/metams/metaMS_plot/.shed.yml b/metams/metaMS_plot/.shed.yml → tools/metams/metaMS_plot/.shed.yml
diff --git a/metams/metaMS_plot/README.rst → tools/metams/metaMS_plot/README.rst b/metams/metaMS_plot/README.rst → tools/metams/metaMS_plot/README.rst
diff --git a/metams/metaMS_plot/lib_metams.r → tools/metams/metaMS_plot/lib_metams.r b/metams/metaMS_plot/lib_metams.r → tools/metams/metaMS_plot/lib_metams.r
diff --git a/metams/metaMS_plot/macros.xml → tools/metams/metaMS_plot/macros.xml b/metams/metaMS_plot/macros.xml → tools/metams/metaMS_plot/macros.xml
diff --git a/metams/metaMS_plot/metaMS_plot.r → tools/metams/metaMS_plot/metaMS_plot.r b/metams/metaMS_plot/metaMS_plot.r → tools/metams/metaMS_plot/metaMS_plot.r
diff --git a/metams/metaMS_plot/metaMS_plot.xml → tools/metams/metaMS_plot/metaMS_plot.xml b/metams/metaMS_plot/metaMS_plot.xml → tools/metams/metaMS_plot/metaMS_plot.xml
diff --git a/...tatic/images/workflow_metaMS_plot.graphml → ...tatic/images/workflow_metaMS_plot.graphml b/...tatic/images/workflow_metaMS_plot.graphml → ...tatic/images/workflow_metaMS_plot.graphml
diff --git a/...ot/static/images/workflow_metaMS_plot.jpg → ...ot/static/images/workflow_metaMS_plot.jpg b/...ot/static/images/workflow_metaMS_plot.jpg → ...ot/static/images/workflow_metaMS_plot.jpg
diff --git a/...ot/static/images/workflow_metaMS_plot.png → ...ot/static/images/workflow_metaMS_plot.png b/...ot/static/images/workflow_metaMS_plot.png → ...ot/static/images/workflow_metaMS_plot.png
diff --git a/metams/metaMS_plot/test-data/BPCs_raw.pdf → ...metams/metaMS_plot/test-data/BPCs_raw.pdf b/metams/metaMS_plot/test-data/BPCs_raw.pdf → ...metams/metaMS_plot/test-data/BPCs_raw.pdf
diff --git a/metams/metaMS_plot/test-data/GCMS_EIC.pdf → ...metams/metaMS_plot/test-data/GCMS_EIC.pdf b/metams/metaMS_plot/test-data/GCMS_EIC.pdf → ...metams/metaMS_plot/test-data/GCMS_EIC.pdf
diff --git a/...s/metaMS_plot/test-data/GCMS_EIC_noDB.pdf → ...s/metaMS_plot/test-data/GCMS_EIC_noDB.pdf b/...s/metaMS_plot/test-data/GCMS_EIC_noDB.pdf → ...s/metaMS_plot/test-data/GCMS_EIC_noDB.pdf
diff --git a/metams/metaMS_plot/test-data/TICs_raw.pdf → ...metams/metaMS_plot/test-data/TICs_raw.pdf b/metams/metaMS_plot/test-data/TICs_raw.pdf → ...metams/metaMS_plot/test-data/TICs_raw.pdf
diff --git a/metams/metaMS_plot/test-data/alg11.mzData → ...metams/metaMS_plot/test-data/alg11.mzData b/metams/metaMS_plot/test-data/alg11.mzData → ...metams/metaMS_plot/test-data/alg11.mzData
diff --git a/metams/metaMS_plot/test-data/alg2.mzData → .../metams/metaMS_plot/test-data/alg2.mzData b/metams/metaMS_plot/test-data/alg2.mzData → .../metams/metaMS_plot/test-data/alg2.mzData
diff --git a/metams/metaMS_plot/test-data/alg3.mzData → .../metams/metaMS_plot/test-data/alg3.mzData b/metams/metaMS_plot/test-data/alg3.mzData → .../metams/metaMS_plot/test-data/alg3.mzData
diff --git a/metams/metaMS_plot/test-data/alg7.mzData → .../metams/metaMS_plot/test-data/alg7.mzData b/metams/metaMS_plot/test-data/alg7.mzData → .../metams/metaMS_plot/test-data/alg7.mzData
diff --git a/metams/metaMS_plot/test-data/alg8.mzData → .../metams/metaMS_plot/test-data/alg8.mzData b/metams/metaMS_plot/test-data/alg8.mzData → .../metams/metaMS_plot/test-data/alg8.mzData
diff --git a/metams/metaMS_plot/test-data/alg9.mzData → .../metams/metaMS_plot/test-data/alg9.mzData b/metams/metaMS_plot/test-data/alg9.mzData → .../metams/metaMS_plot/test-data/alg9.mzData
diff --git a/metams/metaMS_plot/test-data/runGC.RData → .../metams/metaMS_plot/test-data/runGC.RData b/metams/metaMS_plot/test-data/runGC.RData → .../metams/metaMS_plot/test-data/runGC.RData
diff --git a/...ms/metaMS_plot/test-data/runGC_noDB.RData → ...ms/metaMS_plot/test-data/runGC_noDB.RData b/...ms/metaMS_plot/test-data/runGC_noDB.RData → ...ms/metaMS_plot/test-data/runGC_noDB.RData
diff --git a/...ms/metaMS_plot/test-data/runGC_test.RData → ...ms/metaMS_plot/test-data/runGC_test.RData b/...ms/metaMS_plot/test-data/runGC_test.RData → ...ms/metaMS_plot/test-data/runGC_test.RData
diff --git a/metams/metaMS_runGC/.shed.yml → tools/metams/metaMS_runGC/.shed.yml b/metams/metaMS_runGC/.shed.yml → tools/metams/metaMS_runGC/.shed.yml
diff --git a/metams/metaMS_runGC/README.rst → tools/metams/metaMS_runGC/README.rst b/metams/metaMS_runGC/README.rst → tools/metams/metaMS_runGC/README.rst
diff --git a/metams/metaMS_runGC/lib_metams.r → tools/metams/metaMS_runGC/lib_metams.r b/metams/metaMS_runGC/lib_metams.r → tools/metams/metaMS_runGC/lib_metams.r
diff --git a/metams/metaMS_runGC/macros.xml → tools/metams/metaMS_runGC/macros.xml b/metams/metaMS_runGC/macros.xml → tools/metams/metaMS_runGC/macros.xml
diff --git a/metams/metaMS_runGC/metaMS_runGC.r → tools/metams/metaMS_runGC/metaMS_runGC.r b/metams/metaMS_runGC/metaMS_runGC.r → tools/metams/metaMS_runGC/metaMS_runGC.r
diff --git a/metams/metaMS_runGC/metams_runGC.xml → tools/metams/metaMS_runGC/metams_runGC.xml b/metams/metaMS_runGC/metams_runGC.xml → tools/metams/metaMS_runGC/metams_runGC.xml
diff --git a/...atic/images/workflow_metaMS_runGC.graphml → ...atic/images/workflow_metaMS_runGC.graphml b/...atic/images/workflow_metaMS_runGC.graphml → ...atic/images/workflow_metaMS_runGC.graphml
diff --git a/...C/static/images/workflow_metaMS_runGC.jpg → ...C/static/images/workflow_metaMS_runGC.jpg b/...C/static/images/workflow_metaMS_runGC.jpg → ...C/static/images/workflow_metaMS_runGC.jpg
diff --git a/...C/static/images/workflow_metaMS_runGC.png → ...C/static/images/workflow_metaMS_runGC.png b/...C/static/images/workflow_metaMS_runGC.png → ...C/static/images/workflow_metaMS_runGC.png
diff --git a/metams/metaMS_runGC/test-data/RI.csv → tools/metams/metaMS_runGC/test-data/RI.csv b/metams/metaMS_runGC/test-data/RI.csv → tools/metams/metaMS_runGC/test-data/RI.csv
diff --git a/...unGC/test-data/W4M0004_database_small.msp → ...unGC/test-data/W4M0004_database_small.msp b/...unGC/test-data/W4M0004_database_small.msp → ...unGC/test-data/W4M0004_database_small.msp
diff --git a/metams/metaMS_runGC/test-data/alg11.mzData → ...etams/metaMS_runGC/test-data/alg11.mzData b/metams/metaMS_runGC/test-data/alg11.mzData → ...etams/metaMS_runGC/test-data/alg11.mzData
diff --git a/metams/metaMS_runGC/test-data/alg2.mzData → ...metams/metaMS_runGC/test-data/alg2.mzData b/metams/metaMS_runGC/test-data/alg2.mzData → ...metams/metaMS_runGC/test-data/alg2.mzData
diff --git a/metams/metaMS_runGC/test-data/alg3.mzData → ...metams/metaMS_runGC/test-data/alg3.mzData b/metams/metaMS_runGC/test-data/alg3.mzData → ...metams/metaMS_runGC/test-data/alg3.mzData
diff --git a/metams/metaMS_runGC/test-data/alg7.mzData → ...metams/metaMS_runGC/test-data/alg7.mzData b/metams/metaMS_runGC/test-data/alg7.mzData → ...metams/metaMS_runGC/test-data/alg7.mzData
diff --git a/metams/metaMS_runGC/test-data/alg8.mzData → ...metams/metaMS_runGC/test-data/alg8.mzData b/metams/metaMS_runGC/test-data/alg8.mzData → ...metams/metaMS_runGC/test-data/alg8.mzData
diff --git a/metams/metaMS_runGC/test-data/alg9.mzData → ...metams/metaMS_runGC/test-data/alg9.mzData b/metams/metaMS_runGC/test-data/alg9.mzData → ...metams/metaMS_runGC/test-data/alg9.mzData
diff --git a/metams/metaMS_runGC/test-data/dataMatrix.tsv → ...ams/metaMS_runGC/test-data/dataMatrix.tsv b/metams/metaMS_runGC/test-data/dataMatrix.tsv → ...ams/metaMS_runGC/test-data/dataMatrix.tsv
diff --git a/...etaMS_runGC/test-data/dataMatrix_noDB.tsv → ...etaMS_runGC/test-data/dataMatrix_noDB.tsv b/...etaMS_runGC/test-data/dataMatrix_noDB.tsv → ...etaMS_runGC/test-data/dataMatrix_noDB.tsv
diff --git a/...ms/metaMS_runGC/test-data/peakspectra.msp → ...ms/metaMS_runGC/test-data/peakspectra.msp b/...ms/metaMS_runGC/test-data/peakspectra.msp → ...ms/metaMS_runGC/test-data/peakspectra.msp
diff --git a/...taMS_runGC/test-data/peakspectra_noDB.msp → ...taMS_runGC/test-data/peakspectra_noDB.msp b/...taMS_runGC/test-data/peakspectra_noDB.msp → ...taMS_runGC/test-data/peakspectra_noDB.msp
diff --git a/metams/metaMS_runGC/test-data/peaktable.tsv → ...tams/metaMS_runGC/test-data/peaktable.tsv b/metams/metaMS_runGC/test-data/peaktable.tsv → ...tams/metaMS_runGC/test-data/peaktable.tsv
diff --git a/...metaMS_runGC/test-data/peaktable_noDB.tsv → ...metaMS_runGC/test-data/peaktable_noDB.tsv b/...metaMS_runGC/test-data/peaktable_noDB.tsv → ...metaMS_runGC/test-data/peaktable_noDB.tsv
diff --git a/metams/metaMS_runGC/test-data/runGC.RData → ...metams/metaMS_runGC/test-data/runGC.RData b/metams/metaMS_runGC/test-data/runGC.RData → ...metams/metaMS_runGC/test-data/runGC.RData
diff --git a/...s/metaMS_runGC/test-data/runGC_noDB.RData → ...s/metaMS_runGC/test-data/runGC_noDB.RData b/...s/metaMS_runGC/test-data/runGC_noDB.RData → ...s/metaMS_runGC/test-data/runGC_noDB.RData
diff --git a/...metaMS_runGC/test-data/sampleMetadata.tsv → ...metaMS_runGC/test-data/sampleMetadata.tsv b/...metaMS_runGC/test-data/sampleMetadata.tsv → ...metaMS_runGC/test-data/sampleMetadata.tsv
diff --git a/...S_runGC/test-data/sampleMetadata_noDB.tsv → ...S_runGC/test-data/sampleMetadata_noDB.tsv b/...S_runGC/test-data/sampleMetadata_noDB.tsv → ...S_runGC/test-data/sampleMetadata_noDB.tsv
diff --git a/...taMS_runGC/test-data/variableMetadata.tsv → ...taMS_runGC/test-data/variableMetadata.tsv b/...taMS_runGC/test-data/variableMetadata.tsv → ...taMS_runGC/test-data/variableMetadata.tsv
diff --git a/...runGC/test-data/variableMetadata_noDB.tsv → ...runGC/test-data/variableMetadata_noDB.tsv b/...runGC/test-data/variableMetadata_noDB.tsv → ...runGC/test-data/variableMetadata_noDB.tsv
diff --git a/.../metaMS_runGC/test-data/xset_merged.RData → .../metaMS_runGC/test-data/xset_merged.RData b/.../metaMS_runGC/test-data/xset_merged.RData → .../metaMS_runGC/test-data/xset_merged.RData
diff --git a/metams/planemo_shed_update.sh → tools/metams/planemo_shed_update.sh b/metams/planemo_shed_update.sh → tools/metams/planemo_shed_update.sh
diff --git a/metams/planemo_test.sh → tools/metams/planemo_test.sh b/metams/planemo_test.sh → tools/metams/planemo_test.sh
diff --git a/metams/scripts/lib_metams.r → tools/metams/scripts/lib_metams.r b/metams/scripts/lib_metams.r → tools/metams/scripts/lib_metams.r
diff --git a/metams/suite_metaMS/.shed.yml → tools/metams/suite_metaMS/.shed.yml b/metams/suite_metaMS/.shed.yml → tools/metams/suite_metaMS/.shed.yml
diff --git a/.../suite_metaMS/repository_dependencies.xml → .../suite_metaMS/repository_dependencies.xml b/.../suite_metaMS/repository_dependencies.xml → .../suite_metaMS/repository_dependencies.xml
diff --git a/metams/test-data/RI.csv → tools/metams/test-data/RI.csv b/metams/test-data/RI.csv → tools/metams/test-data/RI.csv
diff --git a/metams/test-data/alg11.mzData → tools/metams/test-data/alg11.mzData b/metams/test-data/alg11.mzData → tools/metams/test-data/alg11.mzData
diff --git a/metams/test-data/alg2.mzData → tools/metams/test-data/alg2.mzData b/metams/test-data/alg2.mzData → tools/metams/test-data/alg2.mzData
diff --git a/metams/test-data/alg3.mzData → tools/metams/test-data/alg3.mzData b/metams/test-data/alg3.mzData → tools/metams/test-data/alg3.mzData
diff --git a/metams/test-data/alg7.mzData → tools/metams/test-data/alg7.mzData b/metams/test-data/alg7.mzData → tools/metams/test-data/alg7.mzData
diff --git a/metams/test-data/alg8.mzData → tools/metams/test-data/alg8.mzData b/metams/test-data/alg8.mzData → tools/metams/test-data/alg8.mzData
diff --git a/metams/test-data/alg9.mzData → tools/metams/test-data/alg9.mzData b/metams/test-data/alg9.mzData → tools/metams/test-data/alg9.mzData
diff --git a/metams/test-data/dataMatrix.tsv → tools/metams/test-data/dataMatrix.tsv b/metams/test-data/dataMatrix.tsv → tools/metams/test-data/dataMatrix.tsv
diff --git a/metams/test-data/sampleMetadata.tsv → tools/metams/test-data/sampleMetadata.tsv b/metams/test-data/sampleMetadata.tsv → tools/metams/test-data/sampleMetadata.tsv
diff --git a/metams/test-data/threeStdsDB.msp → tools/metams/test-data/threeStdsDB.msp b/metams/test-data/threeStdsDB.msp → tools/metams/test-data/threeStdsDB.msp
diff --git a/metams/test-data/variableMetadata.tsv → tools/metams/test-data/variableMetadata.tsv b/metams/test-data/variableMetadata.tsv → tools/metams/test-data/variableMetadata.tsv