diff --git a/tool_collections/taxonomy/find_diag_hits/.shed.yml b/legacy/taxonomy/find_diag_hits/.shed.yml similarity index 100% rename from tool_collections/taxonomy/find_diag_hits/.shed.yml rename to legacy/taxonomy/find_diag_hits/.shed.yml diff --git a/tool_collections/taxonomy/find_diag_hits/find_diag_hits.py b/legacy/taxonomy/find_diag_hits/find_diag_hits.py similarity index 100% rename from tool_collections/taxonomy/find_diag_hits/find_diag_hits.py rename to legacy/taxonomy/find_diag_hits/find_diag_hits.py diff --git a/tool_collections/taxonomy/find_diag_hits/find_diag_hits.xml b/legacy/taxonomy/find_diag_hits/find_diag_hits.xml similarity index 100% rename from tool_collections/taxonomy/find_diag_hits/find_diag_hits.xml rename to legacy/taxonomy/find_diag_hits/find_diag_hits.xml diff --git a/tool_collections/taxonomy/find_diag_hits/test-data/find_diag_hits.tabular b/legacy/taxonomy/find_diag_hits/test-data/find_diag_hits.tabular similarity index 100% rename from tool_collections/taxonomy/find_diag_hits/test-data/find_diag_hits.tabular rename to legacy/taxonomy/find_diag_hits/test-data/find_diag_hits.tabular diff --git a/tool_collections/taxonomy/find_diag_hits/test-data/taxonomyGI.taxonomy b/legacy/taxonomy/find_diag_hits/test-data/taxonomyGI.taxonomy similarity index 100% rename from tool_collections/taxonomy/find_diag_hits/test-data/taxonomyGI.taxonomy rename to legacy/taxonomy/find_diag_hits/test-data/taxonomyGI.taxonomy diff --git a/tool_collections/taxonomy/find_diag_hits/tool_dependencies.xml b/legacy/taxonomy/find_diag_hits/tool_dependencies.xml similarity index 100% rename from tool_collections/taxonomy/find_diag_hits/tool_dependencies.xml rename to legacy/taxonomy/find_diag_hits/tool_dependencies.xml diff --git a/tool_collections/taxonomy/gi2taxonomy/.shed.yml b/legacy/taxonomy/gi2taxonomy/.shed.yml similarity index 100% rename from tool_collections/taxonomy/gi2taxonomy/.shed.yml rename to legacy/taxonomy/gi2taxonomy/.shed.yml diff --git a/tool_collections/taxonomy/gi2taxonomy/gi2taxonomy.py b/legacy/taxonomy/gi2taxonomy/gi2taxonomy.py similarity index 100% rename from tool_collections/taxonomy/gi2taxonomy/gi2taxonomy.py rename to legacy/taxonomy/gi2taxonomy/gi2taxonomy.py diff --git a/tool_collections/taxonomy/gi2taxonomy/gi2taxonomy.xml b/legacy/taxonomy/gi2taxonomy/gi2taxonomy.xml similarity index 100% rename from tool_collections/taxonomy/gi2taxonomy/gi2taxonomy.xml rename to legacy/taxonomy/gi2taxonomy/gi2taxonomy.xml diff --git a/tool_collections/taxonomy/gi2taxonomy/test-data/taxonomy2gi-input.tabular b/legacy/taxonomy/gi2taxonomy/test-data/taxonomy2gi-input.tabular similarity index 100% rename from tool_collections/taxonomy/gi2taxonomy/test-data/taxonomy2gi-input.tabular rename to legacy/taxonomy/gi2taxonomy/test-data/taxonomy2gi-input.tabular diff --git a/tool_collections/taxonomy/gi2taxonomy/test-data/taxonomy2gi-output.tabular b/legacy/taxonomy/gi2taxonomy/test-data/taxonomy2gi-output.tabular similarity index 100% rename from tool_collections/taxonomy/gi2taxonomy/test-data/taxonomy2gi-output.tabular rename to legacy/taxonomy/gi2taxonomy/test-data/taxonomy2gi-output.tabular diff --git a/tool_collections/taxonomy/gi2taxonomy/tool_dependencies.xml b/legacy/taxonomy/gi2taxonomy/tool_dependencies.xml similarity index 100% rename from tool_collections/taxonomy/gi2taxonomy/tool_dependencies.xml rename to legacy/taxonomy/gi2taxonomy/tool_dependencies.xml diff --git a/tool_collections/taxonomy/kraken2tax/.shed.yml b/legacy/taxonomy/kraken2tax/.shed.yml similarity index 100% rename from tool_collections/taxonomy/kraken2tax/.shed.yml rename to legacy/taxonomy/kraken2tax/.shed.yml diff --git a/tool_collections/taxonomy/kraken2tax/kraken2tax.xml b/legacy/taxonomy/kraken2tax/kraken2tax.xml similarity index 100% rename from tool_collections/taxonomy/kraken2tax/kraken2tax.xml rename to legacy/taxonomy/kraken2tax/kraken2tax.xml diff --git a/tool_collections/taxonomy/kraken2tax/test-data/kraken2tax-test1.txt b/legacy/taxonomy/kraken2tax/test-data/kraken2tax-test1.txt similarity index 100% rename from tool_collections/taxonomy/kraken2tax/test-data/kraken2tax-test1.txt rename to legacy/taxonomy/kraken2tax/test-data/kraken2tax-test1.txt diff --git a/tool_collections/taxonomy/kraken2tax/test-data/kraken2tax.txt b/legacy/taxonomy/kraken2tax/test-data/kraken2tax.txt similarity index 100% rename from tool_collections/taxonomy/kraken2tax/test-data/kraken2tax.txt rename to legacy/taxonomy/kraken2tax/test-data/kraken2tax.txt diff --git a/tool_collections/taxonomy/kraken2tax/tool-data/ncbi_taxonomy.loc.sample b/legacy/taxonomy/kraken2tax/tool-data/ncbi_taxonomy.loc.sample similarity index 100% rename from tool_collections/taxonomy/kraken2tax/tool-data/ncbi_taxonomy.loc.sample rename to legacy/taxonomy/kraken2tax/tool-data/ncbi_taxonomy.loc.sample diff --git a/tool_collections/taxonomy/kraken2tax/tool_data_table_conf.xml.sample b/legacy/taxonomy/kraken2tax/tool_data_table_conf.xml.sample similarity index 100% rename from tool_collections/taxonomy/kraken2tax/tool_data_table_conf.xml.sample rename to legacy/taxonomy/kraken2tax/tool_data_table_conf.xml.sample diff --git a/tool_collections/taxonomy/kraken2tax/tool_dependencies.xml b/legacy/taxonomy/kraken2tax/tool_dependencies.xml similarity index 100% rename from tool_collections/taxonomy/kraken2tax/tool_dependencies.xml rename to legacy/taxonomy/kraken2tax/tool_dependencies.xml diff --git a/tool_collections/taxonomy/lca_wrapper/.shed.yml b/legacy/taxonomy/lca_wrapper/.shed.yml similarity index 100% rename from tool_collections/taxonomy/lca_wrapper/.shed.yml rename to legacy/taxonomy/lca_wrapper/.shed.yml diff --git a/tool_collections/taxonomy/lca_wrapper/lca.py b/legacy/taxonomy/lca_wrapper/lca.py similarity index 100% rename from tool_collections/taxonomy/lca_wrapper/lca.py rename to legacy/taxonomy/lca_wrapper/lca.py diff --git a/tool_collections/taxonomy/lca_wrapper/lca.xml b/legacy/taxonomy/lca_wrapper/lca.xml similarity index 100% rename from tool_collections/taxonomy/lca_wrapper/lca.xml rename to legacy/taxonomy/lca_wrapper/lca.xml diff --git a/tool_collections/taxonomy/lca_wrapper/test-data/lca_input.taxonomy b/legacy/taxonomy/lca_wrapper/test-data/lca_input.taxonomy similarity index 100% rename from tool_collections/taxonomy/lca_wrapper/test-data/lca_input.taxonomy rename to legacy/taxonomy/lca_wrapper/test-data/lca_input.taxonomy diff --git a/tool_collections/taxonomy/lca_wrapper/test-data/lca_input2.taxonomy b/legacy/taxonomy/lca_wrapper/test-data/lca_input2.taxonomy similarity index 100% rename from tool_collections/taxonomy/lca_wrapper/test-data/lca_input2.taxonomy rename to legacy/taxonomy/lca_wrapper/test-data/lca_input2.taxonomy diff --git a/tool_collections/taxonomy/lca_wrapper/test-data/lca_input3.taxonomy b/legacy/taxonomy/lca_wrapper/test-data/lca_input3.taxonomy similarity index 100% rename from tool_collections/taxonomy/lca_wrapper/test-data/lca_input3.taxonomy rename to legacy/taxonomy/lca_wrapper/test-data/lca_input3.taxonomy diff --git a/tool_collections/taxonomy/lca_wrapper/test-data/lca_output.taxonomy b/legacy/taxonomy/lca_wrapper/test-data/lca_output.taxonomy similarity index 100% rename from tool_collections/taxonomy/lca_wrapper/test-data/lca_output.taxonomy rename to legacy/taxonomy/lca_wrapper/test-data/lca_output.taxonomy diff --git a/tool_collections/taxonomy/lca_wrapper/test-data/lca_output2.taxonomy b/legacy/taxonomy/lca_wrapper/test-data/lca_output2.taxonomy similarity index 100% rename from tool_collections/taxonomy/lca_wrapper/test-data/lca_output2.taxonomy rename to legacy/taxonomy/lca_wrapper/test-data/lca_output2.taxonomy diff --git a/tool_collections/taxonomy/lca_wrapper/test-data/lca_output3.taxonomy b/legacy/taxonomy/lca_wrapper/test-data/lca_output3.taxonomy similarity index 100% rename from tool_collections/taxonomy/lca_wrapper/test-data/lca_output3.taxonomy rename to legacy/taxonomy/lca_wrapper/test-data/lca_output3.taxonomy diff --git a/tool_collections/taxonomy/lca_wrapper/tool_dependencies.xml b/legacy/taxonomy/lca_wrapper/tool_dependencies.xml similarity index 100% rename from tool_collections/taxonomy/lca_wrapper/tool_dependencies.xml rename to legacy/taxonomy/lca_wrapper/tool_dependencies.xml diff --git a/tool_collections/taxonomy/poisson2test/.shed.yml b/legacy/taxonomy/poisson2test/.shed.yml similarity index 100% rename from tool_collections/taxonomy/poisson2test/.shed.yml rename to legacy/taxonomy/poisson2test/.shed.yml diff --git a/tool_collections/taxonomy/poisson2test/poisson2test.py b/legacy/taxonomy/poisson2test/poisson2test.py similarity index 100% rename from tool_collections/taxonomy/poisson2test/poisson2test.py rename to legacy/taxonomy/poisson2test/poisson2test.py diff --git a/tool_collections/taxonomy/poisson2test/poisson2test.xml b/legacy/taxonomy/poisson2test/poisson2test.xml similarity index 100% rename from tool_collections/taxonomy/poisson2test/poisson2test.xml rename to legacy/taxonomy/poisson2test/poisson2test.xml diff --git a/tool_collections/taxonomy/poisson2test/test-data/poisson2test1.tabular b/legacy/taxonomy/poisson2test/test-data/poisson2test1.tabular similarity index 100% rename from tool_collections/taxonomy/poisson2test/test-data/poisson2test1.tabular rename to legacy/taxonomy/poisson2test/test-data/poisson2test1.tabular diff --git a/tool_collections/taxonomy/poisson2test/test-data/poisson2test1_out.tabular b/legacy/taxonomy/poisson2test/test-data/poisson2test1_out.tabular similarity index 100% rename from tool_collections/taxonomy/poisson2test/test-data/poisson2test1_out.tabular rename to legacy/taxonomy/poisson2test/test-data/poisson2test1_out.tabular diff --git a/tool_collections/taxonomy/poisson2test/test-data/poisson2test2.tabular b/legacy/taxonomy/poisson2test/test-data/poisson2test2.tabular similarity index 100% rename from tool_collections/taxonomy/poisson2test/test-data/poisson2test2.tabular rename to legacy/taxonomy/poisson2test/test-data/poisson2test2.tabular diff --git a/tool_collections/taxonomy/poisson2test/test-data/poisson2test2_out.tabular b/legacy/taxonomy/poisson2test/test-data/poisson2test2_out.tabular similarity index 100% rename from tool_collections/taxonomy/poisson2test/test-data/poisson2test2_out.tabular rename to legacy/taxonomy/poisson2test/test-data/poisson2test2_out.tabular diff --git a/tool_collections/taxonomy/poisson2test/tool_dependencies.xml b/legacy/taxonomy/poisson2test/tool_dependencies.xml similarity index 100% rename from tool_collections/taxonomy/poisson2test/tool_dependencies.xml rename to legacy/taxonomy/poisson2test/tool_dependencies.xml diff --git a/tool_collections/taxonomy/t2ps/.shed.yml b/legacy/taxonomy/t2ps/.shed.yml similarity index 100% rename from tool_collections/taxonomy/t2ps/.shed.yml rename to legacy/taxonomy/t2ps/.shed.yml diff --git a/tool_collections/taxonomy/t2ps/t2ps.tgz b/legacy/taxonomy/t2ps/t2ps.tgz similarity index 100% rename from tool_collections/taxonomy/t2ps/t2ps.tgz rename to legacy/taxonomy/t2ps/t2ps.tgz diff --git a/tool_collections/taxonomy/t2ps/t2ps_autoscale.png b/legacy/taxonomy/t2ps/t2ps_autoscale.png similarity index 100% rename from tool_collections/taxonomy/t2ps/t2ps_autoscale.png rename to legacy/taxonomy/t2ps/t2ps_autoscale.png diff --git a/tool_collections/taxonomy/t2ps/t2ps_autoscale_tree.png b/legacy/taxonomy/t2ps/t2ps_autoscale_tree.png similarity index 100% rename from tool_collections/taxonomy/t2ps/t2ps_autoscale_tree.png rename to legacy/taxonomy/t2ps/t2ps_autoscale_tree.png diff --git a/tool_collections/taxonomy/t2ps/t2ps_heatmap.png b/legacy/taxonomy/t2ps/t2ps_heatmap.png similarity index 100% rename from tool_collections/taxonomy/t2ps/t2ps_heatmap.png rename to legacy/taxonomy/t2ps/t2ps_heatmap.png diff --git a/tool_collections/taxonomy/t2ps/t2ps_ideal.png b/legacy/taxonomy/t2ps/t2ps_ideal.png similarity index 100% rename from tool_collections/taxonomy/t2ps/t2ps_ideal.png rename to legacy/taxonomy/t2ps/t2ps_ideal.png diff --git a/tool_collections/taxonomy/t2ps/t2ps_ideal_ssp.png b/legacy/taxonomy/t2ps/t2ps_ideal_ssp.png similarity index 100% rename from tool_collections/taxonomy/t2ps/t2ps_ideal_ssp.png rename to legacy/taxonomy/t2ps/t2ps_ideal_ssp.png diff --git a/tool_collections/taxonomy/t2ps/t2ps_missing_nodes.png b/legacy/taxonomy/t2ps/t2ps_missing_nodes.png similarity index 100% rename from tool_collections/taxonomy/t2ps/t2ps_missing_nodes.png rename to legacy/taxonomy/t2ps/t2ps_missing_nodes.png diff --git a/tool_collections/taxonomy/t2ps/t2ps_node_label.png b/legacy/taxonomy/t2ps/t2ps_node_label.png similarity index 100% rename from tool_collections/taxonomy/t2ps/t2ps_node_label.png rename to legacy/taxonomy/t2ps/t2ps_node_label.png diff --git a/tool_collections/taxonomy/t2ps/t2ps_wrapper.py b/legacy/taxonomy/t2ps/t2ps_wrapper.py similarity index 100% rename from tool_collections/taxonomy/t2ps/t2ps_wrapper.py rename to legacy/taxonomy/t2ps/t2ps_wrapper.py diff --git a/tool_collections/taxonomy/t2ps/t2ps_wrapper.xml b/legacy/taxonomy/t2ps/t2ps_wrapper.xml similarity index 100% rename from tool_collections/taxonomy/t2ps/t2ps_wrapper.xml rename to legacy/taxonomy/t2ps/t2ps_wrapper.xml diff --git a/tool_collections/taxonomy/t2ps/tool_dependencies.xml b/legacy/taxonomy/t2ps/tool_dependencies.xml similarity index 100% rename from tool_collections/taxonomy/t2ps/tool_dependencies.xml rename to legacy/taxonomy/t2ps/tool_dependencies.xml diff --git a/tool_collections/taxonomy/t2t_report/.shed.yml b/legacy/taxonomy/t2t_report/.shed.yml similarity index 100% rename from tool_collections/taxonomy/t2t_report/.shed.yml rename to legacy/taxonomy/t2t_report/.shed.yml diff --git a/tool_collections/taxonomy/t2t_report/t2t_report.xml b/legacy/taxonomy/t2t_report/t2t_report.xml similarity index 100% rename from tool_collections/taxonomy/t2t_report/t2t_report.xml rename to legacy/taxonomy/t2t_report/t2t_report.xml diff --git a/tool_collections/taxonomy/t2t_report/test-data/t2t_report.tabular b/legacy/taxonomy/t2t_report/test-data/t2t_report.tabular similarity index 100% rename from tool_collections/taxonomy/t2t_report/test-data/t2t_report.tabular rename to legacy/taxonomy/t2t_report/test-data/t2t_report.tabular diff --git a/tool_collections/taxonomy/t2t_report/test-data/taxonomyGI.taxonomy b/legacy/taxonomy/t2t_report/test-data/taxonomyGI.taxonomy similarity index 100% rename from tool_collections/taxonomy/t2t_report/test-data/taxonomyGI.taxonomy rename to legacy/taxonomy/t2t_report/test-data/taxonomyGI.taxonomy diff --git a/tool_collections/taxonomy/t2t_report/tool_dependencies.xml b/legacy/taxonomy/t2t_report/tool_dependencies.xml similarity index 100% rename from tool_collections/taxonomy/t2t_report/tool_dependencies.xml rename to legacy/taxonomy/t2t_report/tool_dependencies.xml