diff --git a/scripts/fix-lockfile.py b/scripts/fix-lockfile.py
new file mode 100644
index 0000000..60f400a
--- /dev/null
+++ b/scripts/fix-lockfile.py
@@ -0,0 +1,65 @@
+import yaml
+import os
+import copy
+import argparse
+
+
+def update_file(fn, dry):
+    with open(fn, 'r') as handle:
+        unlocked = yaml.safe_load(handle)
+    # If a lock file exists, load it from that file
+    if os.path.exists(fn + '.lock'):
+        with open(fn + '.lock', 'r') as handle:
+            locked = yaml.safe_load(handle)
+    else:
+        # Otherwise just clone the "unlocked" list.
+        locked = copy.deepcopy(unlocked)
+
+    # We will place entries in a cleaned lockfile, removing defunct entries, etc.
+    clean_lockfile = copy.deepcopy(locked)
+    clean_lockfile['tools'] = []
+
+    # As here we add any new tools in.
+    for tool in unlocked['tools']:
+        # If we have an existing locked copy, we'll just use that.
+        locked_tools = [x for x in locked['tools'] if x['name'] == tool['name'] and x['owner'] == tool['owner']]
+        # If there are no copies of it seen in the lockfile, we'll just copy it
+        # over directly, without a reivision. Another script will fix that.
+        if len(locked) == 0:
+            # new tool, just add directly.
+            clean_lockfile['tools'].append(tool)
+            continue
+
+        # Otherwise we hvae one or more locked versions so we'll harmonise +
+        # reduce. Revisions are the only thing that could be variable.
+        # Name/section/owner should not be. If they are, we take original human
+        # edited .yaml file as source of truth.
+
+        revisions = []
+        for locked_tool in locked_tools:
+            for revision in locked_tool.get('revisions', []):
+                revisions.append(revision)
+
+        new_tool = {
+            'name': tool['name'],
+            'owner': tool['owner'],
+            'revisions': sorted(list(set(revisions))),  # Cast to list for yaml serialization
+        }
+        if tool.get('tool_panel_section_id'):
+            new_tool.update({'tool_panel_section_id': tool['tool_panel_section_id']})
+        if tool.get('tool_panel_section_label'):
+            new_tool.update({'tool_panel_section_label': tool['tool_panel_section_label']})
+
+        clean_lockfile['tools'].append(new_tool)
+
+    with open(fn + '.lock', 'w') as handle:
+        yaml.dump(clean_lockfile, handle, default_flow_style=False)
+
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('fn', type=argparse.FileType('r'), help="Tool.yaml file")
+    parser.add_argument('--dry-run', action='store_true', help="Trust all listed tools in the file, i.e. add the latest changest for them.")
+    args = parser.parse_args()
+    update_file(args.fn.name, dry=args.dry_run)
diff --git a/scripts/update-tool.py b/scripts/update-tool.py
new file mode 100644
index 0000000..dce9d86
--- /dev/null
+++ b/scripts/update-tool.py
@@ -0,0 +1,72 @@
+import yaml
+import os
+import glob
+import copy
+import argparse
+import logging
+
+from bioblend import toolshed
+
+ts = toolshed.ToolShedInstance(url='https://toolshed.g2.bx.psu.edu')
+
+
+def update_file(fn, owner=None, name=None, without=False):
+    with open(fn + '.lock', 'r') as handle:
+        locked = yaml.safe_load(handle)
+
+    # Update any locked tools.
+    for tool in locked['tools']:
+        # If without, then if it is lacking, we should exec.
+        logging.debug("Examining {owner}/{name}".format(**tool))
+
+        if without:
+            if 'revisions' in tool and not len(tool.get('revisions', [])) == 0:
+                continue
+
+        if not without and owner and tool['owner'] != owner:
+            continue
+
+        if not without and name and tool['name'] != name:
+            continue
+
+        logging.info("Fetching updates for {owner}/{name}".format(**tool))
+
+        try:
+            revs = ts.repositories.get_ordered_installable_revisions(tool['name'], tool['owner'])
+        except Exception as e:
+            print(e)
+            continue
+
+        logging.debug('TS revisions: %s' % ','.join(revs))
+        latest_rev = revs[-1]
+        if latest_rev in tool.get('revisions', []):
+            # The rev is already known, don't add again.
+            continue
+
+        logging.info("Found newer revision of {owner}/{name} ({rev})".format(rev=latest_rev, **tool))
+
+        # Get latest rev, if not already added, add it.
+        if 'revisions' not in tool:
+            tool['revisions'] = []
+
+        if latest_rev not in tool['revisions']:
+            # TS doesn't support utf8 and we don't want to either.
+            tool['revisions'].append(str(latest_rev))
+
+        tool['revisions'] = sorted(list(set( tool['revisions'] )))
+
+    with open(fn + '.lock', 'w') as handle:
+        yaml.dump(locked, handle, default_flow_style=False)
+
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('fn', type=argparse.FileType('r'), help="Tool.yaml file")
+    parser.add_argument('--owner', help="Repository owner to filter on, anything matching this will be updated")
+    parser.add_argument('--name', help="Repository name to filter on, anything matching this will be updated")
+    parser.add_argument('--without', action='store_true', help="If supplied will ignore any owner/name and just automatically add the latest hash for anything lacking one.")
+    parser.add_argument('--log', choices=('critical', 'error', 'warning', 'info', 'debug'), default='info')
+    args = parser.parse_args()
+    logging.basicConfig(level=getattr(logging, args.log.upper()))
+    update_file(args.fn.name, owner=args.owner, name=args.name, without=args.without)
diff --git a/umsa_tool_list.yaml b/umsa_tool_list.yaml
index 25f2dca..a71dde7 100644
--- a/umsa_tool_list.yaml
+++ b/umsa_tool_list.yaml
@@ -194,12 +194,6 @@ tools:
   - 4e3b2049a4d3
   tool_panel_section_label: ChemicalToolBox
   tool_shed_url: toolshed.g2.bx.psu.edu
-- name: query
-  owner: recetox
-  revisions:
-  - 0369de831b32
-  tool_panel_section_label: ChemicalToolBox
-  tool_shed_url: testtoolshed.g2.bx.psu.edu
 - name: msconvert
   owner: galaxyp
   revisions:
@@ -1196,6 +1190,12 @@ tools:
   - da15e8ea3b28
   tool_panel_section_label: matchms
   tool_shed_url: toolshed.g2.bx.psu.edu
+- name: matchms_remove_spectra
+  owner: recetox
+  revisions:
+  -  80df426e7e47
+  tool_panel_section_label: matchms
+  tool_shed_url: toolshed.g2.bx.psu.edu
 - name: matchms_split
   owner: recetox
   revisions:
diff --git a/umsa_tool_list.yaml.lock b/umsa_tool_list.yaml.lock
new file mode 100644
index 0000000..4005883
--- /dev/null
+++ b/umsa_tool_list.yaml.lock
@@ -0,0 +1,1131 @@
+tools:
+- name: collapse_collections
+  owner: nml
+  revisions:
+  - 90981f86000f
+  tool_panel_section_label: Collection Operations
+- name: scatterplot
+  owner: devteam
+  revisions:
+  - efda9a4a50e7
+  tool_panel_section_label: Visualization
+- name: ggplot2_violin
+  owner: iuc
+  revisions:
+  - 0e7290688b50
+  - dfd5d981b5a4
+  tool_panel_section_label: Visualization
+- name: ggplot2_heatmap
+  owner: iuc
+  revisions:
+  - 10515715c940
+  - 391a4cc45fea
+  tool_panel_section_label: Visualization
+- name: ggplot2_pca
+  owner: iuc
+  revisions:
+  - 7e616a1bdb07
+  - b1268b7544d3
+  tool_panel_section_label: Visualization
+- name: ggplot2_histogram
+  owner: iuc
+  revisions:
+  - 398e5104f8a2
+  - b0d96516e6a5
+  tool_panel_section_label: Visualization
+- name: ggplot2_heatmap2
+  owner: iuc
+  revisions:
+  - 374e9062d874
+  - ca7cb0eaad62
+  tool_panel_section_label: Visualization
+- name: ggplot2_point
+  owner: iuc
+  revisions:
+  - 3b12bf9b4b87
+  - e3a675da7fd0
+  tool_panel_section_label: Visualization
+- name: datamash_transpose
+  owner: iuc
+  revisions:
+  - 22c2a1ac7ae3
+  - a513e3fbb4c5
+  tool_panel_section_label: Text Manipulation
+- name: diff
+  owner: bgruening
+  revisions:
+  - 156d0908e232
+  - 95a9dc82fc9a
+  tool_panel_section_label: Text Manipulation
+- name: text_processing
+  owner: bgruening
+  revisions:
+  - ddf54b12c295
+  - fbf99087e067
+  tool_panel_section_label: Text Manipulation
+- name: split_file_on_column
+  owner: bgruening
+  revisions:
+  - ff2a81aa3f08
+  tool_panel_section_label: Filter and Sort
+- name: recetox_msfinder
+  owner: recetox
+  revisions:
+  - e7eff0c9baa3
+  tool_panel_section_label: RECETOX
+- name: rem_complex
+  owner: recetox
+  revisions:
+  - 1dc9f5a3163d
+  - 567327a97ad2
+  - a0e07a0bc047
+  tool_panel_section_label: RECETOX
+- name: msmetaenhancer
+  owner: recetox
+  revisions:
+  - 3e2cb0bc6959
+  - b5467dead5b1
+  tool_panel_section_label: RECETOX
+- name: xtb_molecular_optimization
+  owner: recetox
+  revisions:
+  - d5633eaf3552
+  tool_panel_section_label: RECETOX
+- name: recetox_xmsannotator_advanced
+  owner: recetox
+  revisions:
+  - 6b5dec818827
+  - cfd2e19f00a9
+  tool_panel_section_label: RECETOX
+- name: waveica
+  owner: recetox
+  revisions:
+  - 071a424241ec
+  - 6480c6d5fa36
+  tool_panel_section_label: RECETOX
+- name: ramclustr
+  owner: recetox
+  revisions:
+  - 050cfef6ba65
+  - da7722f665f4
+  tool_panel_section_label: RECETOX
+- name: rmassbank
+  owner: recetox
+  revisions:
+  - 0b28816c1c2c
+  - 5a6bb93ec656
+  tool_panel_section_label: RECETOX
+- name: biotransformer
+  owner: recetox
+  revisions:
+  - 0b86600b715e
+  - e5fcba090b10
+  tool_panel_section_label: RECETOX
+- name: spec2vec_training
+  owner: recetox
+  revisions:
+  - 9d917de87cca
+  - e1e22ada831e
+  tool_panel_section_label: RECETOX
+- name: riassigner
+  owner: recetox
+  revisions:
+  - af25aa61c611
+  - c702620c22b1
+  tool_panel_section_label: RECETOX
+- name: assign_ri_from_comment
+  owner: recetox
+  revisions:
+  - 6975af39ba79
+  - 7226eba9c09d
+  - 97ccdb1ba47c
+  tool_panel_section_label: RECETOX
+- name: ramclustr_define_experiment
+  owner: recetox
+  revisions:
+  - 25625114618e
+  - f2c1d0bbb074
+  tool_panel_section_label: RECETOX
+- name: msp_split
+  owner: recetox
+  revisions:
+  - ae0263faa819
+  tool_panel_section_label: RECETOX
+- name: filter_compounds
+  owner: recetox
+  revisions:
+  - 6c5df3eeb768
+  - 72b687d21f65
+  tool_panel_section_label: RECETOX
+- name: thermo_raw_file_converter
+  owner: galaxyp
+  revisions:
+  - 19e45916daf9
+  tool_panel_section_label: RECETOX
+- name: camera_annotate
+  owner: lecorguille
+  revisions:
+  - 4b9ab71be05e
+  - abf1775ac14d
+  tool_panel_section_label: CAMERA
+- name: camera_combinexsannos
+  owner: mmonsoor
+  revisions:
+  - 961089e21ae2
+  tool_panel_section_label: CAMERA
+- name: rem_complex
+  owner: recetox
+  revisions:
+  - 1dc9f5a3163d
+  - 567327a97ad2
+  - a0e07a0bc047
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_remions
+  owner: bgruening
+  revisions:
+  - 4e3b2049a4d3
+  tool_panel_section_label: ChemicalToolBox
+- name: query
+  owner: recetox
+  revisions:
+  - 0369de831b32
+  tool_panel_section_label: ChemicalToolBox
+- name: msconvert
+  owner: galaxyp
+  revisions:
+  - 545054b15d7c
+  - 6153e8ada1ee
+  tool_panel_section_label: ChemicalToolBox
+- name: smina
+  owner: earlhaminst
+  revisions:
+  - 7c0bb0c48a27
+  tool_panel_section_label: ChemicalToolBox
+- name: apoc
+  owner: earlhaminst
+  revisions:
+  - 451f90534945
+  - 67d2a6f3b4e3
+  tool_panel_section_label: ChemicalToolBox
+- name: parmconv
+  owner: chemteam
+  revisions:
+  - 6c6cecf51bd0
+  - 6d0677a148fe
+  tool_panel_section_label: ChemicalToolBox
+- name: enumerate_charges
+  owner: bgruening
+  revisions:
+  - 36360fa103d6
+  - 67ee76f0e497
+  tool_panel_section_label: ChemicalToolBox
+- name: sdf_to_tab
+  owner: bgruening
+  revisions:
+  - 4beb3e026bbb
+  - 55553120df69
+  tool_panel_section_label: ChemicalToolBox
+- name: fpocket
+  owner: bgruening
+  revisions:
+  - 4cc9d85c3bae
+  - 4fb73be7f4cb
+  tool_panel_section_label: ChemicalToolBox
+- name: chembl_structure_pipeline
+  owner: bgruening
+  revisions:
+  - 2f59c6239f25
+  tool_panel_section_label: ChemicalToolBox
+- name: chembl
+  owner: bgruening
+  revisions:
+  - 1d6fb7967ae9
+  - a446ea7e2bc1
+  tool_panel_section_label: ChemicalToolBox
+- name: ambertools_parmchk2
+  owner: chemteam
+  revisions:
+  - 96b872138d3b
+  - ecc43bf27a49
+  tool_panel_section_label: ChemicalToolBox
+- name: ambertools_antechamber
+  owner: chemteam
+  revisions:
+  - 29aa7091e533
+  - 8a839e6a1e3e
+  tool_panel_section_label: ChemicalToolBox
+- name: ambertools_acpype
+  owner: chemteam
+  revisions:
+  - 095ad4d096d1
+  - f4230f116196
+  tool_panel_section_label: ChemicalToolBox
+- name: mordred
+  owner: bgruening
+  revisions:
+  - cc0f89287ecf
+  tool_panel_section_label: ChemicalToolBox
+- name: get_pdb
+  owner: bgruening
+  revisions:
+  - 538790c6c21b
+  tool_panel_section_label: ChemicalToolBox
+- name: get_pubchem
+  owner: bgruening
+  revisions:
+  - 4d966d5bdd17
+  tool_panel_section_label: ChemicalToolBox
+- name: get_online_data
+  owner: bgruening
+  revisions:
+  - 2538366eb8fb
+  tool_panel_section_label: ChemicalToolBox
+- name: autodock_vina
+  owner: bgruening
+  revisions:
+  - 7a871df65202
+  - 90ea16534012
+  tool_panel_section_label: ChemicalToolBox
+- name: autodock_vina_prepare_ligand
+  owner: bgruening
+  revisions:
+  - 50871000e977
+  tool_panel_section_label: ChemicalToolBox
+- name: autodock_vina_prepare_box
+  owner: bgruening
+  revisions:
+  - 8f766d9652a2
+  - ad35eaa204ea
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_remduplicates
+  owner: bgruening
+  revisions:
+  - 50ca8845e7f5
+  - b2569e22b40c
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_addh
+  owner: bgruening
+  revisions:
+  - 43167f164076
+  - 6e4b7e0c61a6
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_filter
+  owner: bgruening
+  revisions:
+  - df4dc55197dd
+  - ff2dd4b7d918
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_subsearch
+  owner: bgruening
+  revisions:
+  - 171c94786a56
+  - c19608db6b15
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_compound_convert
+  owner: bgruening
+  revisions:
+  - 1c66bf08f687
+  - e2c36f62e22f
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_remove_protonation_state
+  owner: bgruening
+  revisions:
+  - bf4e668b6690
+  - e376ba0fcde0
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_spectrophore_search
+  owner: bgruening
+  revisions:
+  - 330514267c57
+  - afd14e10a318
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_svg_depiction
+  owner: bgruening
+  revisions:
+  - 7672039a0bb0
+  - d3b48303045b
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_multi_obgrep
+  owner: bgruening
+  revisions:
+  - 09640954740c
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_genprop
+  owner: bgruening
+  revisions:
+  - a72ae2711a97
+  - b249bf9be0d1
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_change_title
+  owner: bgruening
+  revisions:
+  - 01ab890bf0ad
+  - 3ecaa9634126
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_obgrep
+  owner: bgruening
+  revisions:
+  - 274193d6c443
+  - 78640d0127ce
+  tool_panel_section_label: ChemicalToolBox
+- name: openbabel_remsmall
+  owner: bgruening
+  revisions:
+  - aebc671bae78
+  - d7f0ca1f2669
+  tool_panel_section_label: ChemicalToolBox
+- name: prepare_ligands_for_docking
+  owner: bgruening
+  revisions:
+  - 5486f7a2b0cb
+  - de4c80d17527
+  tool_panel_section_label: ChemicalToolBox
+- name: biomd_neqgamma
+  owner: chemteam
+  revisions:
+  - 4f3222cb5cf6
+  - afcb925def69
+  tool_panel_section_label: ChemicalToolBox
+- name: biomd_rmsd_clustering
+  owner: chemteam
+  revisions:
+  - b001ebc8bf58
+  - b9c46dbe9605
+  tool_panel_section_label: ChemicalToolBox
+- name: biomd_extract_clusters
+  owner: chemteam
+  revisions:
+  - 078dfd7fb26d
+  - e0ecaf2d05fb
+  tool_panel_section_label: ChemicalToolBox
+- name: fastpca
+  owner: chemteam
+  revisions:
+  - 6f2029791c94
+  - 9ca30ad95444
+  tool_panel_section_label: ChemicalToolBox
+- name: bio3d_dccm
+  owner: chemteam
+  revisions:
+  - c9ae0c833ded
+  tool_panel_section_label: ChemicalToolBox
+- name: bio3d_pca_visualize
+  owner: chemteam
+  revisions:
+  - f61a718993fd
+  tool_panel_section_label: ChemicalToolBox
+- name: bio3d_pca
+  owner: chemteam
+  revisions:
+  - 24867ab16f36
+  tool_panel_section_label: ChemicalToolBox
+- name: bio3d_rmsd
+  owner: chemteam
+  revisions:
+  - 77e28e1da9f4
+  tool_panel_section_label: ChemicalToolBox
+- name: bio3d_rmsf
+  owner: chemteam
+  revisions:
+  - 6bcb804a54c3
+  tool_panel_section_label: ChemicalToolBox
+- name: mdanalysis_extract_rmsd
+  owner: chemteam
+  revisions:
+  - 589f8ef21e58
+  - 743bd6aa3c7a
+  tool_panel_section_label: ChemicalToolBox
+- name: mdanalysis_ramachandran_protein
+  owner: chemteam
+  revisions:
+  - 060b9d9ec8cf
+  - 0f270722aca6
+  tool_panel_section_label: ChemicalToolBox
+- name: mdanalysis_endtoend
+  owner: chemteam
+  revisions:
+  - 78aa3659fcd1
+  - 795a5996cdc8
+  tool_panel_section_label: ChemicalToolBox
+- name: mdanalysis_cosine_analysis
+  owner: chemteam
+  revisions:
+  - 48d6a6eb438b
+  - a842da7ef42b
+  tool_panel_section_label: ChemicalToolBox
+- name: vmd_hbonds
+  owner: chemteam
+  revisions:
+  - 8aa5e465b043
+  tool_panel_section_label: ChemicalToolBox
+- name: mdanalysis_hbonds
+  owner: chemteam
+  revisions:
+  - 4c36f5ad2799
+  - b17ce46509ad
+  tool_panel_section_label: ChemicalToolBox
+- name: mdanalysis_ramachandran_plot
+  owner: chemteam
+  revisions:
+  - 70a2d548e62c
+  - be5eaea0b2d1
+  tool_panel_section_label: ChemicalToolBox
+- name: mdanalysis_distance
+  owner: chemteam
+  revisions:
+  - fd987ff06ceb
+  - ffd6f8d159e1
+  tool_panel_section_label: ChemicalToolBox
+- name: mdanalysis_dihedral
+  owner: chemteam
+  revisions:
+  - 976cfd44b921
+  - aaa130695a2b
+  tool_panel_section_label: ChemicalToolBox
+- name: mdanalysis_rdf
+  owner: chemteam
+  revisions:
+  - 1a220575ad7a
+  - 49076afc90b1
+  tool_panel_section_label: ChemicalToolBox
+- name: mdanalysis_angle
+  owner: chemteam
+  revisions:
+  - 567f8c5d4680
+  - a0d210b9d287
+  tool_panel_section_label: ChemicalToolBox
+- name: packmol
+  owner: chemteam
+  revisions:
+  - 539fb45630e6
+  tool_panel_section_label: ChemicalToolBox
+- name: ctb_rdkit_descriptors
+  owner: bgruening
+  revisions:
+  - 0993ac4f4a23
+  - cf725c82c865
+  tool_panel_section_label: ChemicalToolBox
+- name: alchemical_analysis
+  owner: chemteam
+  revisions:
+  - c1fa72716efc
+  tool_panel_section_label: ChemicalToolBox
+- name: gmx_editconf
+  owner: chemteam
+  revisions:
+  - 88076940fa94
+  - bfb65cb551d8
+  tool_panel_section_label: ChemicalToolBox
+- name: gmx_makendx
+  owner: chemteam
+  revisions:
+  - d9eb276dfa32
+  - e3e536aa2633
+  tool_panel_section_label: ChemicalToolBox
+- name: gmx_restraints
+  owner: chemteam
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