Workflows with tools not in toolshed

As a followup on my PR #1709, there were tools in workflows I could not attach the correct tool_shed_repository to:

Topic | Tutorial | Tutorial name | Tutorial file name | Tool name [Tool id] that does not exist in toolshed
-- | -- | -- | -- | --
proteomics | secretome-prediction | Secreted Proteins via GO annotation and WoLF PSORT for shCTSB paper | WF_secretomePrediction_goWolfpsort.ga | Get all the term IDs and term names of a given OBO ontology[term_id_vs_term_name], Get subontology from a given OBO term[get_subontology_from]
~computational-chemistry~ | ~cheminformatics~ | ~CTB workflow~ |~main_workflow.ga~ | ~NxN Clustering[testtoolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering/0.1], Remove duplicated molecules[testtoolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remDuplicates/1.0], Compound Search[testtoolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_obgrep/0.1], Natural Product[testtoolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator/0.1], Compound Convert[testtoolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_compound_convert/0.1], Remove counterions and fragments[testtoolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons/1.0], Change Title[testtoolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_change_title/0.0.1]~
computational-chemistry | md-simulation-namd | MD_NAMD | main_workflow.ga | NAMD MD Simulator (NPT)[namd_npt], Energy Minimizer[minimizer], NAMD MD Simulator (NVT)[namd_nvt], System Setup[setup]
computational-chemistry | md-simulation-namd | NAMD_MD_from_CHARMM-GUI | main_workflow_charmmgui.ga | NAMD MD Simulator (NPT)[namd_npt], NAMD MD Simulator (NVT)[namd_nvt]

The second one is off course because they are still in the test tool shed.

Start with WF_secretomePrediction_goWolfpsort.ga and the main_workflow.ga and main_workflow_charmmgui.ga files named in the issue. Inspect the listed tool references and compare them with the available Tool Shed entries, noting which remain in the test shed. Done means the affected workflows have valid, intentionally handled tool references.

Written by the indexing model from the issue text.