diff --git a/metams/macros/macros.xml b/tools/metams/macros/macros.xml similarity index 100% rename from metams/macros/macros.xml rename to tools/metams/macros/macros.xml diff --git a/metams/metaMS_plot/.shed.yml b/tools/metams/metaMS_plot/.shed.yml similarity index 100% rename from metams/metaMS_plot/.shed.yml rename to tools/metams/metaMS_plot/.shed.yml diff --git a/metams/metaMS_plot/README.rst b/tools/metams/metaMS_plot/README.rst similarity index 100% rename from metams/metaMS_plot/README.rst rename to tools/metams/metaMS_plot/README.rst diff --git a/metams/metaMS_plot/lib_metams.r b/tools/metams/metaMS_plot/lib_metams.r similarity index 100% rename from metams/metaMS_plot/lib_metams.r rename to tools/metams/metaMS_plot/lib_metams.r diff --git a/metams/metaMS_plot/macros.xml b/tools/metams/metaMS_plot/macros.xml similarity index 100% rename from metams/metaMS_plot/macros.xml rename to tools/metams/metaMS_plot/macros.xml diff --git a/metams/metaMS_plot/metaMS_plot.r b/tools/metams/metaMS_plot/metaMS_plot.r similarity index 100% rename from metams/metaMS_plot/metaMS_plot.r rename to tools/metams/metaMS_plot/metaMS_plot.r diff --git a/metams/metaMS_plot/metaMS_plot.xml b/tools/metams/metaMS_plot/metaMS_plot.xml similarity index 100% rename from metams/metaMS_plot/metaMS_plot.xml rename to tools/metams/metaMS_plot/metaMS_plot.xml diff --git a/metams/metaMS_plot/static/images/workflow_metaMS_plot.graphml b/tools/metams/metaMS_plot/static/images/workflow_metaMS_plot.graphml similarity index 100% rename from metams/metaMS_plot/static/images/workflow_metaMS_plot.graphml rename to tools/metams/metaMS_plot/static/images/workflow_metaMS_plot.graphml diff --git a/metams/metaMS_plot/static/images/workflow_metaMS_plot.jpg b/tools/metams/metaMS_plot/static/images/workflow_metaMS_plot.jpg similarity index 100% rename from metams/metaMS_plot/static/images/workflow_metaMS_plot.jpg rename to tools/metams/metaMS_plot/static/images/workflow_metaMS_plot.jpg diff --git a/metams/metaMS_plot/static/images/workflow_metaMS_plot.png b/tools/metams/metaMS_plot/static/images/workflow_metaMS_plot.png similarity index 100% rename from metams/metaMS_plot/static/images/workflow_metaMS_plot.png rename to tools/metams/metaMS_plot/static/images/workflow_metaMS_plot.png diff --git a/metams/metaMS_plot/test-data/BPCs_raw.pdf b/tools/metams/metaMS_plot/test-data/BPCs_raw.pdf similarity index 100% rename from metams/metaMS_plot/test-data/BPCs_raw.pdf rename to tools/metams/metaMS_plot/test-data/BPCs_raw.pdf diff --git a/metams/metaMS_plot/test-data/GCMS_EIC.pdf b/tools/metams/metaMS_plot/test-data/GCMS_EIC.pdf similarity index 100% rename from metams/metaMS_plot/test-data/GCMS_EIC.pdf rename to tools/metams/metaMS_plot/test-data/GCMS_EIC.pdf diff --git a/metams/metaMS_plot/test-data/GCMS_EIC_noDB.pdf b/tools/metams/metaMS_plot/test-data/GCMS_EIC_noDB.pdf similarity index 100% rename from metams/metaMS_plot/test-data/GCMS_EIC_noDB.pdf rename to tools/metams/metaMS_plot/test-data/GCMS_EIC_noDB.pdf diff --git a/metams/metaMS_plot/test-data/TICs_raw.pdf b/tools/metams/metaMS_plot/test-data/TICs_raw.pdf similarity index 100% rename from metams/metaMS_plot/test-data/TICs_raw.pdf rename to tools/metams/metaMS_plot/test-data/TICs_raw.pdf diff --git a/metams/metaMS_plot/test-data/alg11.mzData b/tools/metams/metaMS_plot/test-data/alg11.mzData similarity index 100% rename from metams/metaMS_plot/test-data/alg11.mzData rename to tools/metams/metaMS_plot/test-data/alg11.mzData diff --git a/metams/metaMS_plot/test-data/alg2.mzData b/tools/metams/metaMS_plot/test-data/alg2.mzData similarity index 100% rename from metams/metaMS_plot/test-data/alg2.mzData rename to tools/metams/metaMS_plot/test-data/alg2.mzData diff --git a/metams/metaMS_plot/test-data/alg3.mzData b/tools/metams/metaMS_plot/test-data/alg3.mzData similarity index 100% rename from metams/metaMS_plot/test-data/alg3.mzData rename to tools/metams/metaMS_plot/test-data/alg3.mzData diff --git a/metams/metaMS_plot/test-data/alg7.mzData b/tools/metams/metaMS_plot/test-data/alg7.mzData similarity index 100% rename from metams/metaMS_plot/test-data/alg7.mzData rename to tools/metams/metaMS_plot/test-data/alg7.mzData diff --git a/metams/metaMS_plot/test-data/alg8.mzData b/tools/metams/metaMS_plot/test-data/alg8.mzData similarity index 100% rename from metams/metaMS_plot/test-data/alg8.mzData rename to tools/metams/metaMS_plot/test-data/alg8.mzData diff --git a/metams/metaMS_plot/test-data/alg9.mzData b/tools/metams/metaMS_plot/test-data/alg9.mzData similarity index 100% rename from metams/metaMS_plot/test-data/alg9.mzData rename to tools/metams/metaMS_plot/test-data/alg9.mzData diff --git a/metams/metaMS_plot/test-data/runGC.RData b/tools/metams/metaMS_plot/test-data/runGC.RData similarity index 100% rename from metams/metaMS_plot/test-data/runGC.RData rename to tools/metams/metaMS_plot/test-data/runGC.RData diff --git a/metams/metaMS_plot/test-data/runGC_noDB.RData b/tools/metams/metaMS_plot/test-data/runGC_noDB.RData similarity index 100% rename from metams/metaMS_plot/test-data/runGC_noDB.RData rename to tools/metams/metaMS_plot/test-data/runGC_noDB.RData diff --git a/metams/metaMS_plot/test-data/runGC_test.RData b/tools/metams/metaMS_plot/test-data/runGC_test.RData similarity index 100% rename from metams/metaMS_plot/test-data/runGC_test.RData rename to tools/metams/metaMS_plot/test-data/runGC_test.RData diff --git a/metams/metaMS_runGC/.shed.yml b/tools/metams/metaMS_runGC/.shed.yml similarity index 100% rename from metams/metaMS_runGC/.shed.yml rename to tools/metams/metaMS_runGC/.shed.yml diff --git a/metams/metaMS_runGC/README.rst b/tools/metams/metaMS_runGC/README.rst similarity index 100% rename from metams/metaMS_runGC/README.rst rename to tools/metams/metaMS_runGC/README.rst diff --git a/metams/metaMS_runGC/lib_metams.r b/tools/metams/metaMS_runGC/lib_metams.r similarity index 100% rename from metams/metaMS_runGC/lib_metams.r rename to tools/metams/metaMS_runGC/lib_metams.r diff --git a/metams/metaMS_runGC/macros.xml b/tools/metams/metaMS_runGC/macros.xml similarity index 100% rename from metams/metaMS_runGC/macros.xml rename to tools/metams/metaMS_runGC/macros.xml diff --git a/metams/metaMS_runGC/metaMS_runGC.r b/tools/metams/metaMS_runGC/metaMS_runGC.r similarity index 100% rename from metams/metaMS_runGC/metaMS_runGC.r rename to tools/metams/metaMS_runGC/metaMS_runGC.r diff --git a/metams/metaMS_runGC/metams_runGC.xml b/tools/metams/metaMS_runGC/metams_runGC.xml similarity index 100% rename from metams/metaMS_runGC/metams_runGC.xml rename to tools/metams/metaMS_runGC/metams_runGC.xml diff --git a/metams/metaMS_runGC/static/images/workflow_metaMS_runGC.graphml b/tools/metams/metaMS_runGC/static/images/workflow_metaMS_runGC.graphml similarity index 100% rename from metams/metaMS_runGC/static/images/workflow_metaMS_runGC.graphml rename to tools/metams/metaMS_runGC/static/images/workflow_metaMS_runGC.graphml diff --git a/metams/metaMS_runGC/static/images/workflow_metaMS_runGC.jpg b/tools/metams/metaMS_runGC/static/images/workflow_metaMS_runGC.jpg similarity index 100% rename from metams/metaMS_runGC/static/images/workflow_metaMS_runGC.jpg rename to tools/metams/metaMS_runGC/static/images/workflow_metaMS_runGC.jpg diff --git a/metams/metaMS_runGC/static/images/workflow_metaMS_runGC.png b/tools/metams/metaMS_runGC/static/images/workflow_metaMS_runGC.png similarity index 100% rename from metams/metaMS_runGC/static/images/workflow_metaMS_runGC.png rename to tools/metams/metaMS_runGC/static/images/workflow_metaMS_runGC.png diff --git a/metams/metaMS_runGC/test-data/RI.csv b/tools/metams/metaMS_runGC/test-data/RI.csv similarity index 100% rename from metams/metaMS_runGC/test-data/RI.csv rename to tools/metams/metaMS_runGC/test-data/RI.csv diff --git a/metams/metaMS_runGC/test-data/W4M0004_database_small.msp b/tools/metams/metaMS_runGC/test-data/W4M0004_database_small.msp similarity index 100% rename from metams/metaMS_runGC/test-data/W4M0004_database_small.msp rename to tools/metams/metaMS_runGC/test-data/W4M0004_database_small.msp diff --git a/metams/metaMS_runGC/test-data/alg11.mzData b/tools/metams/metaMS_runGC/test-data/alg11.mzData similarity index 100% rename from metams/metaMS_runGC/test-data/alg11.mzData rename to tools/metams/metaMS_runGC/test-data/alg11.mzData diff --git a/metams/metaMS_runGC/test-data/alg2.mzData b/tools/metams/metaMS_runGC/test-data/alg2.mzData similarity index 100% rename from metams/metaMS_runGC/test-data/alg2.mzData rename to tools/metams/metaMS_runGC/test-data/alg2.mzData diff --git a/metams/metaMS_runGC/test-data/alg3.mzData b/tools/metams/metaMS_runGC/test-data/alg3.mzData similarity index 100% rename from metams/metaMS_runGC/test-data/alg3.mzData rename to tools/metams/metaMS_runGC/test-data/alg3.mzData diff --git a/metams/metaMS_runGC/test-data/alg7.mzData b/tools/metams/metaMS_runGC/test-data/alg7.mzData similarity index 100% rename from metams/metaMS_runGC/test-data/alg7.mzData rename to tools/metams/metaMS_runGC/test-data/alg7.mzData diff --git a/metams/metaMS_runGC/test-data/alg8.mzData b/tools/metams/metaMS_runGC/test-data/alg8.mzData similarity index 100% rename from metams/metaMS_runGC/test-data/alg8.mzData rename to tools/metams/metaMS_runGC/test-data/alg8.mzData diff --git a/metams/metaMS_runGC/test-data/alg9.mzData b/tools/metams/metaMS_runGC/test-data/alg9.mzData similarity index 100% rename from metams/metaMS_runGC/test-data/alg9.mzData rename to tools/metams/metaMS_runGC/test-data/alg9.mzData diff --git a/metams/metaMS_runGC/test-data/dataMatrix.tsv b/tools/metams/metaMS_runGC/test-data/dataMatrix.tsv similarity index 100% rename from metams/metaMS_runGC/test-data/dataMatrix.tsv rename to tools/metams/metaMS_runGC/test-data/dataMatrix.tsv diff --git a/metams/metaMS_runGC/test-data/dataMatrix_noDB.tsv b/tools/metams/metaMS_runGC/test-data/dataMatrix_noDB.tsv similarity index 100% rename from metams/metaMS_runGC/test-data/dataMatrix_noDB.tsv rename to tools/metams/metaMS_runGC/test-data/dataMatrix_noDB.tsv diff --git a/metams/metaMS_runGC/test-data/peakspectra.msp b/tools/metams/metaMS_runGC/test-data/peakspectra.msp similarity index 100% rename from metams/metaMS_runGC/test-data/peakspectra.msp rename to tools/metams/metaMS_runGC/test-data/peakspectra.msp diff --git a/metams/metaMS_runGC/test-data/peakspectra_noDB.msp b/tools/metams/metaMS_runGC/test-data/peakspectra_noDB.msp similarity index 100% rename from metams/metaMS_runGC/test-data/peakspectra_noDB.msp rename to tools/metams/metaMS_runGC/test-data/peakspectra_noDB.msp diff --git a/metams/metaMS_runGC/test-data/peaktable.tsv b/tools/metams/metaMS_runGC/test-data/peaktable.tsv similarity index 100% rename from metams/metaMS_runGC/test-data/peaktable.tsv rename to tools/metams/metaMS_runGC/test-data/peaktable.tsv diff --git a/metams/metaMS_runGC/test-data/peaktable_noDB.tsv b/tools/metams/metaMS_runGC/test-data/peaktable_noDB.tsv similarity index 100% rename from metams/metaMS_runGC/test-data/peaktable_noDB.tsv rename to tools/metams/metaMS_runGC/test-data/peaktable_noDB.tsv diff --git a/metams/metaMS_runGC/test-data/runGC.RData b/tools/metams/metaMS_runGC/test-data/runGC.RData similarity index 100% rename from metams/metaMS_runGC/test-data/runGC.RData rename to tools/metams/metaMS_runGC/test-data/runGC.RData diff --git a/metams/metaMS_runGC/test-data/runGC_noDB.RData b/tools/metams/metaMS_runGC/test-data/runGC_noDB.RData similarity index 100% rename from metams/metaMS_runGC/test-data/runGC_noDB.RData rename to tools/metams/metaMS_runGC/test-data/runGC_noDB.RData diff --git a/metams/metaMS_runGC/test-data/sampleMetadata.tsv b/tools/metams/metaMS_runGC/test-data/sampleMetadata.tsv similarity index 100% rename from metams/metaMS_runGC/test-data/sampleMetadata.tsv rename to tools/metams/metaMS_runGC/test-data/sampleMetadata.tsv diff --git a/metams/metaMS_runGC/test-data/sampleMetadata_noDB.tsv b/tools/metams/metaMS_runGC/test-data/sampleMetadata_noDB.tsv similarity index 100% rename from metams/metaMS_runGC/test-data/sampleMetadata_noDB.tsv rename to tools/metams/metaMS_runGC/test-data/sampleMetadata_noDB.tsv diff --git a/metams/metaMS_runGC/test-data/variableMetadata.tsv b/tools/metams/metaMS_runGC/test-data/variableMetadata.tsv similarity index 100% rename from metams/metaMS_runGC/test-data/variableMetadata.tsv rename to tools/metams/metaMS_runGC/test-data/variableMetadata.tsv diff --git a/metams/metaMS_runGC/test-data/variableMetadata_noDB.tsv b/tools/metams/metaMS_runGC/test-data/variableMetadata_noDB.tsv similarity index 100% rename from metams/metaMS_runGC/test-data/variableMetadata_noDB.tsv rename to tools/metams/metaMS_runGC/test-data/variableMetadata_noDB.tsv diff --git a/metams/metaMS_runGC/test-data/xset_merged.RData b/tools/metams/metaMS_runGC/test-data/xset_merged.RData similarity index 100% rename from metams/metaMS_runGC/test-data/xset_merged.RData rename to tools/metams/metaMS_runGC/test-data/xset_merged.RData diff --git a/metams/planemo_shed_update.sh b/tools/metams/planemo_shed_update.sh similarity index 100% rename from metams/planemo_shed_update.sh rename to tools/metams/planemo_shed_update.sh diff --git a/metams/planemo_test.sh b/tools/metams/planemo_test.sh similarity index 100% rename from metams/planemo_test.sh rename to tools/metams/planemo_test.sh diff --git a/metams/scripts/lib_metams.r b/tools/metams/scripts/lib_metams.r similarity index 100% rename from metams/scripts/lib_metams.r rename to tools/metams/scripts/lib_metams.r diff --git a/metams/suite_metaMS/.shed.yml b/tools/metams/suite_metaMS/.shed.yml similarity index 100% rename from metams/suite_metaMS/.shed.yml rename to tools/metams/suite_metaMS/.shed.yml diff --git a/metams/suite_metaMS/repository_dependencies.xml b/tools/metams/suite_metaMS/repository_dependencies.xml similarity index 100% rename from metams/suite_metaMS/repository_dependencies.xml rename to tools/metams/suite_metaMS/repository_dependencies.xml diff --git a/metams/test-data/RI.csv b/tools/metams/test-data/RI.csv similarity index 100% rename from metams/test-data/RI.csv rename to tools/metams/test-data/RI.csv diff --git a/metams/test-data/alg11.mzData b/tools/metams/test-data/alg11.mzData similarity index 100% rename from metams/test-data/alg11.mzData rename to tools/metams/test-data/alg11.mzData diff --git a/metams/test-data/alg2.mzData b/tools/metams/test-data/alg2.mzData similarity index 100% rename from metams/test-data/alg2.mzData rename to tools/metams/test-data/alg2.mzData diff --git a/metams/test-data/alg3.mzData b/tools/metams/test-data/alg3.mzData similarity index 100% rename from metams/test-data/alg3.mzData rename to tools/metams/test-data/alg3.mzData diff --git a/metams/test-data/alg7.mzData b/tools/metams/test-data/alg7.mzData similarity index 100% rename from metams/test-data/alg7.mzData rename to tools/metams/test-data/alg7.mzData diff --git a/metams/test-data/alg8.mzData b/tools/metams/test-data/alg8.mzData similarity index 100% rename from metams/test-data/alg8.mzData rename to tools/metams/test-data/alg8.mzData diff --git a/metams/test-data/alg9.mzData b/tools/metams/test-data/alg9.mzData similarity index 100% rename from metams/test-data/alg9.mzData rename to tools/metams/test-data/alg9.mzData diff --git a/metams/test-data/dataMatrix.tsv b/tools/metams/test-data/dataMatrix.tsv similarity index 100% rename from metams/test-data/dataMatrix.tsv rename to tools/metams/test-data/dataMatrix.tsv diff --git a/metams/test-data/sampleMetadata.tsv b/tools/metams/test-data/sampleMetadata.tsv similarity index 100% rename from metams/test-data/sampleMetadata.tsv rename to tools/metams/test-data/sampleMetadata.tsv diff --git a/metams/test-data/threeStdsDB.msp b/tools/metams/test-data/threeStdsDB.msp similarity index 100% rename from metams/test-data/threeStdsDB.msp rename to tools/metams/test-data/threeStdsDB.msp diff --git a/metams/test-data/variableMetadata.tsv b/tools/metams/test-data/variableMetadata.tsv similarity index 100% rename from metams/test-data/variableMetadata.tsv rename to tools/metams/test-data/variableMetadata.tsv