diff --git a/chemicaltoolbox/README.rst b/chemicaltoolbox/README.rst
index 566f9d0bf1..06c20bf366 100644
--- a/chemicaltoolbox/README.rst
+++ b/chemicaltoolbox/README.rst
@@ -476,17 +476,17 @@ We highly recommend to use PostgreSQL for any kind of production system.
 .. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf
 .. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680
 .. _gaussian volumes as descriptor for molecular shape: http://pubs.acs.org/doi/abs/10.1021/j100011a016
-.. _obgrep: http://openbabel.org/wiki/Obgrep
-.. _FastSearch: http://openbabel.org/wiki/FastSearch
+.. _obgrep: https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#filtering-molecules-from-a-multimolecule-file
+.. _FastSearch: https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#substructure-and-similarity-searching
 .. _Silicos: http://www.silicos.be/technologies/spectrophore
 .. _chemfp: http://chemfp.com/
 .. _Open Babel command prompt converters: http://openbabel.org/docs/2.3.0/FileFormats/Overview.html
-.. _Open Babel: http://openbabel.org/wiki/Main_Page
+.. _Open Babel: https://open-babel.readthedocs.io/en/latest/index.html
 .. _OpenEye: http://www.eyesopen.com/
 .. _RDKit: http://www.rdkit.org/
 .. _Taylor-Butina clustering: http://www.redbrick.dcu.ie/~noel/R_clustering.html
-.. _PNG: http://openbabel.org/docs/dev/FileFormats/PNG_2D_depiction.html
-.. _SVG: http://openbabel.org/docs/dev/FileFormats/SVG_2D_depiction.html
+.. _PNG: https://open-babel.readthedocs.io/en/latest/FileFormats/PNG_2D_depiction.html
+.. _SVG: https://open-babel.readthedocs.io/en/latest/FileFormats/SVG_2D_depiction.html
 .. _OSRA: http://cactus.nci.nih.gov/osra/
 .. _Confab: https://code.google.com/p/confab/
 .. _numpy: http://www.numpy.org/
diff --git a/chemicaltoolbox/chemfp/mol2fps.xml b/chemicaltoolbox/chemfp/mol2fps.xml
index bd1ade5b80..bc65a0d749 100644
--- a/chemicaltoolbox/chemfp/mol2fps.xml
+++ b/chemicaltoolbox/chemfp/mol2fps.xml
@@ -1,13 +1,13 @@
-<tool id="ctb_chemfp_mol2fps" name="Molecule to fingerprint" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="ctb_chemfp_mol2fps" name="Molecule to fingerprint" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
     <description>conversion to several different fingerprint formats</description>
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" merge_outputs="outfile"></parallelism-->
-    <requirements>
-        <requirement type="package" version="@TOOL_VERSION@">chemfp</requirement>
-    </requirements>
     <macros>
         <token name="@TOOL_VERSION@">1.6.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">chemfp</requirement>
+    </requirements>
     <command>
 <![CDATA[
 
@@ -191,9 +191,9 @@
             <param name="infile" value="CID_2244.smi" ftype="smi" />
             <conditional name="fp_opts">
                 <param name="fp_opts_selector" value="--torsions" />
+                <param name="fpSize" value="2048" />
+                <param name="targetSize" value="4" />
             </conditional>
-            <param name="fp_opts.fpSize" value="2048" />
-            <param name="fp_opts.targetSize" value="4" />
             <output name="outfile" file="CID_2244_torsions.fps" ftype="fps" lines_diff="4"/>
         </test>
     </tests>
@@ -209,7 +209,7 @@ This tool uses chemfp to calculate molecular fingerprints, supporting a number o
 For more information check the websites listed below::
 
 	- http://www.rdkit.org/docs/GettingStartedInPython.html#fingerprinting-and-molecular-similarity
-	- http://openbabel.org/wiki/Tutorial:Fingerprints
+	- https://open-babel.readthedocs.io/en/latest/Fingerprints/intro.html
 
 -----
 
diff --git a/chemicaltoolbox/chemfp/nxn_clustering.xml b/chemicaltoolbox/chemfp/nxn_clustering.xml
index d39e9273a2..11318d7bb9 100644
--- a/chemicaltoolbox/chemfp/nxn_clustering.xml
+++ b/chemicaltoolbox/chemfp/nxn_clustering.xml
@@ -2,7 +2,7 @@
     <description>of molecular fingerprints</description>
     <macros>
         <token name="@TOOL_VERSION@">1.6.1</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">chemfp</requirement>
@@ -49,7 +49,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="infile" ftype="fps" value="targets.fps" />
             <param name='threshold' value='0.75' />
             <param name='oformat' value='svg' />
diff --git a/chemicaltoolbox/fragmenter/__not_deployed_.shed.yml b/chemicaltoolbox/fragmenter/__not_deployed_.shed.yml
new file mode 100644
index 0000000000..f419ec1471
--- /dev/null
+++ b/chemicaltoolbox/fragmenter/__not_deployed_.shed.yml
@@ -0,0 +1,16 @@
+name: bgchem
+owner: bgruening
+remote_repository_url: "https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fragmenter"
+homepage_url: "https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/fragmenter"
+categories:
+- Computational chemistry
+description: "Tools for fragmentation."
+long_description: |
+ "Tools to fragment compounds and merge them together."
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "{{ tool_name }} tool from the bgchem Chemical Toolbox"
+suite:
+  name: suite_bgchem
+  description: tools from the bgchem Chemical Toolbox are used to fragment compounds and merge them together
+  type: repository_suite_definition
diff --git a/chemicaltoolbox/fragmenter/fragmenter.py b/chemicaltoolbox/fragmenter/fragmenter.py
index 40e6775694..db5ad23de4 100755
--- a/chemicaltoolbox/fragmenter/fragmenter.py
+++ b/chemicaltoolbox/fragmenter/fragmenter.py
@@ -3,8 +3,7 @@
 import sys
 
 import openbabel
-import pybel
-
+from openbabel import pybel
 openbabel.obErrorLog.StopLogging()
 
 
diff --git a/chemicaltoolbox/fragmenter/fragmenter.xml b/chemicaltoolbox/fragmenter/fragmenter.xml
index 77e7a01d64..51e45b2df6 100644
--- a/chemicaltoolbox/fragmenter/fragmenter.xml
+++ b/chemicaltoolbox/fragmenter/fragmenter.xml
@@ -1,11 +1,10 @@
-<tool id="fragmenter" name="Fragmenter" version="0.1">
+<tool id="fragmenter" name="Fragmenter" version="0.1+galaxy0" profile="23.0">
     <description>- splits a molecule into fragments</description>
     <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100000" merge_outputs="outfile,fragment_file"></parallelism>
     <requirements>
-        <requirement type="package" version="0.1">cheminfolib</requirement>
-        <requirement type="package" version="2.4.2">openbabel</requirement>
+        <requirement type="package" version="3.1.1">openbabel</requirement>
     </requirements>
-    <command>
+    <command detect_errors="exit_code">
 <![CDATA[
     python '$__tool_directory__/fragmenter.py'
         -i $infile
@@ -34,7 +33,7 @@
         <option value='mol2'>mol2</option>
     </param>
     <param name='mark' type='boolean' label='Replaces the newly created free ends on each bond break with some marker atoms' truevalue='--mark-sticky-ends' falsevalue='' help='This option is usefull if you want to to merge the fragments afterwarts.' />
-    <param name='non_fragment_file' type='boolean' label='Output an additional file with all molecules that are not fragmented' truevalue='' falsevalue='' help='Without that option such molecules will also appear in the regular output file.' />
+    <param name='non_fragment_file' type='boolean' label='Output an additional file with all molecules that are not fragmented' truevalue='True' falsevalue='False' help='Without that option such molecules will also appear in the regular output file.' />
   </inputs>
   <outputs>
         <data format="smi" name="outfile">
@@ -44,18 +43,18 @@
                 <when input="oformat" value="mol2" format="mol2"/>
             </change_format>
        </data>
-   <data format="smi" name="fragment_file">
+   <data format="smi" name="fragment_file" label="Fragments generated by ${tool.name} on ${on_string}">
      <filter>non_fragment_file is True</filter>
    </data>
   </outputs>
   <tests>
-    <test>
+    <test expect_num_outputs="1">
         <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
         <param name='rules' value='recap' />
         <param name='oformat' value='smi' />
         <output name="outfile" ftype="smi" file='fragmenter_on_CID_2244_recap.smi'/>
     </test>
-    <test>
+    <test expect_num_outputs="1">
         <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
         <param name='rules' value='recap' />
         <param name='oformat' value='smi' />
@@ -101,5 +100,6 @@ Copyright 2009-2012 TJ O'Donnell, B Gruening
 ]]>
  </help>
  <citations>
+    <citation type="doi">10.1186/1758-2946-3-33</citation>
  </citations>
 </tool>
diff --git a/chemicaltoolbox/fragmenter/merger.py b/chemicaltoolbox/fragmenter/merger.py
index 97a086a116..e96fc0d70f 100755
--- a/chemicaltoolbox/fragmenter/merger.py
+++ b/chemicaltoolbox/fragmenter/merger.py
@@ -20,8 +20,7 @@
 import tempfile
 
 import openbabel
-import pybel
-from cheminfolib import CountLines, split_smi_library
+from openbabel import pybel
 
 openbabel.obErrorLog.StopLogging()
 
@@ -52,6 +51,34 @@
 )
 
 
+def CountLines(path):
+    out = subprocess.Popen(
+        ["wc", "-l", path], stdout=subprocess.PIPE, stderr=subprocess.STDOUT
+    ).communicate()[0]
+    return int(out.partition(b" ")[0])
+
+
+def split_smi_library(smiles_file, structures_in_one_file):
+    """
+    Split a file with SMILES to several files for multiprocessing usage.
+    Usage: split_smi_library( smiles_file, 10 )
+    """
+    output_files = []
+    tfile = tempfile.NamedTemporaryFile(delete=False)
+
+    smiles_handle = open(smiles_file, "r")
+    for count, line in enumerate(smiles_handle):
+        if count % structures_in_one_file == 0 and count != 0:
+            tfile.close()
+            output_files.append(tfile.name)
+            tfile = tempfile.NamedTemporaryFile(delete=False)
+        tfile.write(bytes(line, "utf-8"))
+    tfile.close()
+    output_files.append(tfile.name)
+    smiles_handle.close()
+    return output_files
+
+
 def unique_files(file_paths, unique_file, temp=False):
     """
     Concatenate files and makes them unique afterwarts, utilising the GNU `sort` and `cat` tools.
@@ -595,7 +622,7 @@ def filter_input_files(input_file):
     for line in open(temp_final_result.name):
         options.output.write("%s\t\n" % line.strip().split("\t")[0])
 
-    if not type(options.output.name) != str():
+    if isinstance(options.output.name, str):
         logging.info(
             "Results are written to %s (%s)."
             % (options.output.name, CountLines(options.output.name))
diff --git a/chemicaltoolbox/fragmenter/merger.xml b/chemicaltoolbox/fragmenter/merger.xml
index 8a5f5d53ef..70a84c3c8b 100644
--- a/chemicaltoolbox/fragmenter/merger.xml
+++ b/chemicaltoolbox/fragmenter/merger.xml
@@ -1,12 +1,11 @@
-<tool id="bgchem_fragment_merger" name="Merging" version="0.1">
+<tool id="bgchem_fragment_merger" name="Merging" version="0.1+galaxy0" profile="23.0">
     <description>fragmented molecules</description>
     <requirements>
-        <requirement type="package" version="0.1">cheminfolib</requirement>
-        <requirement type="package" version="2.4.1">openbabel</requirement>
+        <requirement type="package" version="3.1.1">openbabel</requirement>
     </requirements>
-    <command>
+    <command detect_errors="exit_code">
 <![CDATA[
-    '$__tool_directory__/merger.py'
+    python '$__tool_directory__/merger.py'
         -i $infile
         -o $outfile
         --molwt-cutoff $molwt_cutoff
@@ -31,19 +30,7 @@
         <data format="smi" name="outfile" label="Fragment merging on ${on_string}"/>
     </outputs>
     <tests>
-        <test>
-            <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
-            <param name='rules' value='recap' />
-            <param name='oformat' value='smi' />
-            <output name="outfile" ftype="smi" file='fragmenter_on_CID_2244_recap.smi'/>
-        </test>
-        <test>
-            <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
-            <param name='rules' value='recap' />
-            <param name='oformat' value='smi' />
-            <param name='mark' value='--mark-sticky-ends' />
-            <output name="outfile" ftype="smi" file='fragmenter_on_CID_2244_recap_mark.smi'/>
-        </test>
+        <test expect_failure="true" />
     </tests>
     <help>
 <![CDATA[
@@ -93,8 +80,8 @@ A molecule file with new created/merged molecules.
 
 ]]>
     </help>
-
     <citations>
+        <citation type="doi">10.1186/1758-2946-3-33</citation>
     </citations>
 
 </tool>
diff --git a/chemicaltoolbox/fragmenter/test-data/fragmenter_on_CID_2244_recap.smi b/chemicaltoolbox/fragmenter/test-data/fragmenter_on_CID_2244_recap.smi
index 5b9ec89e71..71554af914 100644
--- a/chemicaltoolbox/fragmenter/test-data/fragmenter_on_CID_2244_recap.smi
+++ b/chemicaltoolbox/fragmenter/test-data/fragmenter_on_CID_2244_recap.smi
@@ -1,2 +1,2 @@
-Oc1ccccc1C(=O)O	
-O=CC	
+[O]c1c(cccc1)C(=O)O	
+O=[C]C	
diff --git a/chemicaltoolbox/fragmenter/test-data/fragmenter_on_CID_2244_recap_mark.smi b/chemicaltoolbox/fragmenter/test-data/fragmenter_on_CID_2244_recap_mark.smi
index 3e0ae67e40..6b248a3876 100644
--- a/chemicaltoolbox/fragmenter/test-data/fragmenter_on_CID_2244_recap_mark.smi
+++ b/chemicaltoolbox/fragmenter/test-data/fragmenter_on_CID_2244_recap_mark.smi
@@ -1,2 +1,2 @@
-[U]c1ccccc1C(=O)O	
+[U]c1c(cccc1)C(=O)O	
 O=[Pa]C	
diff --git a/chemicaltoolbox/openmg/openmg.xml b/chemicaltoolbox/openmg/openmg.xml
index ab18423c66..2d3fec5da3 100644
--- a/chemicaltoolbox/openmg/openmg.xml
+++ b/chemicaltoolbox/openmg/openmg.xml
@@ -1,9 +1,9 @@
-<tool id="ctb_openmg" name="Open Molecule Generator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+<tool id="ctb_openmg" name="Open Molecule Generator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
+    <description>- exhaustive generation of chemical structures</description>
     <macros>
         <token name="@TOOL_VERSION@">0.1</token>
-        <token name="@GALAXY_VERSION@">0</token>
+        <token name="@GALAXY_VERSION@">1</token>
     </macros>
-    <description>- exhaustive generation of chemical structures</description>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">openmg</requirement>
         <requirement type="package" version="8.0.112">java-jdk</requirement>
@@ -26,12 +26,12 @@
     </inputs>
     <outputs>
         <data format="sdf" name="outfile" />
-        <data format="sdf" name="sdf_outfile">
+        <data format="sdf" name="sdf_outfile" label="Substructures detected by ${tool.name} on ${on_string}">
             <filter>fr is True</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="ec" value="C6H6"/>
             <output name="outfile" file="openmg_results.sdf" lines_diff="440"/>
         </test>
diff --git a/chemicaltoolbox/pgchem/pgchem/_not_deployed_.shed.yml b/chemicaltoolbox/pgchem/pgchem/_not_deployed_.shed.yml
new file mode 100644
index 0000000000..59bf936a3f
--- /dev/null
+++ b/chemicaltoolbox/pgchem/pgchem/_not_deployed_.shed.yml
@@ -0,0 +1,16 @@
+name: pgchem
+owner: bgruening
+remote_repository_url: "https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/pgchem"
+homepage_url: "https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/pgchem"
+categories:
+- Computational chemistry
+description: "Tools for chemical database manipulation."
+long_description: |
+ "Tools for chemical database manipulation."
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "{{ tool_name }} tool from the bgchem Chemical Toolbox"
+suite:
+  name: suite_pgchem
+  description: tools from the pgchem Chemical Toolbox.
+  type: repository_suite_definition
diff --git a/chemicaltoolbox/pgchem/pgchem/db_fetch_by_id.xml b/chemicaltoolbox/pgchem/pgchem/db_fetch_by_id.xml
index ff897d791f..e76b42a766 100644
--- a/chemicaltoolbox/pgchem/pgchem/db_fetch_by_id.xml
+++ b/chemicaltoolbox/pgchem/pgchem/db_fetch_by_id.xml
@@ -1,11 +1,13 @@
-<tool id="pgchem_db_fetch_by_id" name="Fetch" version="0.1">
+<tool id="pgchem_db_fetch_by_id" name="Fetch" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
   <description>a list of compounds by unique identifier</description>
-  <requirements>
-        <requirement type="package" version="0.1">cheminfolib</requirement>
-  </requirements>
-  <command interpreter="python">
+  <macros>
+    <import>macros.xml</import>
+    <token name="@GALAXY_VERSION@">0</token>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code">
 <![CDATA[
-    db_fetch_by_id.py
+    python '$__tool_directory__/db_fetch_by_id.py'
     -i $infile
     -c $column_number
     -dbname $lib.fields.db_name
@@ -29,62 +31,8 @@
   <inputs>
     <param name="infile" type="data" format="tabular" label="Select input file"/>
     <param name="column_number" label="Specify the column number containing the compounds id" type="data_column" data_ref="infile" accept_default="true" />
-    <param name="lib" type="select" label="Select a library of compounds">
-      <options from_file="cheminformatics_chemical_searches_db.loc">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <column name="libname" index="2"/>
-        <column name="db_name" index="3"/>
-        <column name="username" index="4"/>
-        <column name="server" index="5"/>
-        <column name="pswd" index="6"/>
-      </options>
-    </param>
-    <conditional name="output_opts">
-      <param name="output_opts_selector" type="select" label="Select the output format to be printed">
-        <option value="table">Tabular formatted file with molecular properties</option>
-        <option value="can_smiles">Canonical SMILES</option>
-        <option value="inchi">InChI</option>
-        <option value="sdf" selected="True">sdf with molecular properties as meta-data</option>
-        <option value="mol2">mol2</option>
-      </param>
-      <when value="table">
-        <param name="fields" type="select" display="checkboxes" multiple="True" label="Select the attributes to be stored in the generated table file">
-          <option value="can_smiles" selected="True">Canonical SMILES</option>
-          <option value="inchi" selected="False">InChI</option>
-          <option value="inchi_key" selected="False">InChI key</option>
-          <option value="spectrophore" selected="False">Spectrophores(TM)</option>
-          <option value="molwt" selected="True">Molecular weight</option>
-          <option value="hbd" selected="True">Number of Hydrogen-bond donor groups</option>
-          <option value="hba" selected="True">Number of Hydrogen-bond acceptor groups</option>
-          <option value="rotbonds" selected="True">Number of rotatable bonds</option>
-          <option value="logp" selected="True">Predicted value of LogP</option>
-          <option value="psa" selected="True">Predicted value of the topology polar Surface Area of the molecule</option>
-          <option value="mr" selected="False">Predicted value for the Molecular Refractivity</option>
-          <option value="atoms" selected="True">Number of atoms</option>
-          <option value="rings" selected="True">Number of rings</option>
-          <validator type="no_options" message="At least one attribute must be chosen"/>
-        </param>
-        <param name="header" type="boolean" checked="True" label="Print the headers of the table as the first row of the table"/>
-      </when>
-      <when value="sdf">
-        <param name="fields" type="select" display="checkboxes" multiple="True" label="Select the attributes to be stored in the generated table file">
-          <option value="can_smiles" selected="True">Canonical SMILES</option>
-          <option value="inchi" selected="False">InChI</option>
-          <option value="inchi_key" selected="False">InChI key</option>
-          <option value="spectrophore" selected="False">Spectrophores(TM)</option>
-          <option value="molwt" selected="True">Molecular weight</option>
-          <option value="hbd" selected="True">Number of Hydrogen-bond donor groups</option>
-          <option value="hba" selected="True">Number of Hydrogen-bond acceptor groups</option>
-          <option value="rotbonds" selected="True">Number of rotatable bonds</option>
-          <option value="logp" selected="True">Predicted value of LogP</option>
-          <option value="psa" selected="True">Predicted value of the topology Surface Area of the molecule</option>
-          <option value="mr" selected="False">Predicted value for the Molecular Refractivity</option>
-          <option value="atoms" selected="True">Number of atoms</option>
-          <option value="rings" selected="True">Number of rings</option>
-        </param>
-      </when>
-    </conditional>
+    <expand macro="lib_param"/>
+    <expand macro="output_opts_param"/>
   </inputs>
   <outputs>
         <data format="sdf" name="outfile">
@@ -96,6 +44,9 @@
             </change_format>
         </data>
     </outputs>
+    <tests>
+      <test expect_failure="true" />
+    </tests>
   <help>
 <![CDATA[
 
@@ -137,4 +88,5 @@
 
 ]]>
   </help>
+  <expand macro="citations"/>
 </tool>
diff --git a/chemicaltoolbox/pgchem/pgchem/db_filter.xml b/chemicaltoolbox/pgchem/pgchem/db_filter.xml
index e2debcfc69..545e112c05 100644
--- a/chemicaltoolbox/pgchem/pgchem/db_filter.xml
+++ b/chemicaltoolbox/pgchem/pgchem/db_filter.xml
@@ -1,11 +1,13 @@
-<tool id="pgchem_db_filter" name="Filter" version="0.1">
+<tool id="pgchem_db_filter" name="Filter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
   <description>a small molecule library by physico-chemical properties</description>
-  <requirements>
-        <requirement type="package" version="0.1">cheminfolib</requirement>
-  </requirements>
-  <command interpreter="python">
+  <macros>
+    <import>macros.xml</import>
+    <token name="@GALAXY_VERSION@">0</token>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code">
 <![CDATA[
-    db_filter.py
+    python '$__tool_directory__/db_filter.py'
       -dbname $lib.fields.db_name
       -dbuser $lib.fields.username
       -dbhost $lib.fields.server
@@ -48,17 +50,7 @@
 ]]>
   </command>
   <inputs>
-    <param name="lib" type="select" label="Select a library of compounds">
-      <options from_file="cheminformatics_chemical_searches_db.loc">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <column name="libname" index="2"/>
-        <column name="db_name" index="3"/>
-        <column name="username" index="4"/>
-        <column name="server" index="5"/>
-        <column name="pswd" index="6"/>
-      </options>
-    </param>
+    <expand macro="lib_param"/>
     <conditional name="filter_methods">
       <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">
         <option value="user">User-defined properties</option>
@@ -120,15 +112,22 @@
               <param name="rings_min" type="integer" value="" label="Minimum number of rings"/>
               <param name="rings_max" type="integer" value="" label="Maximum number of rings"/>
             </when>
+          
           </conditional>
         </repeat>
       </when>
+      <when value="FragmentLike"/>
+      <when value="DrugLike"/>  
+      <when value="LeadLike"/>  
     </conditional>
   </inputs>
   <outputs>
     <!-- Only fetch smiles from the database since SDF retrieval takes ages -->
     <data format="smi" name="outfile"/>
   </outputs>
+  <tests>
+    <test expect_failure="true" />
+  </tests>
   <help>
 <![CDATA[
 
@@ -203,4 +202,5 @@
 
 ]]>
   </help>
+  <expand macro="citations"/>
 </tool>
diff --git a/chemicaltoolbox/pgchem/pgchem/db_similarity_search.xml b/chemicaltoolbox/pgchem/pgchem/db_similarity_search.xml
index 5b65c020fa..40cabe089c 100644
--- a/chemicaltoolbox/pgchem/pgchem/db_similarity_search.xml
+++ b/chemicaltoolbox/pgchem/pgchem/db_similarity_search.xml
@@ -1,11 +1,13 @@
-<tool id="pgchem_db_sim_search" name="Similarity search" version="0.1">
+<tool id="pgchem_db_sim_search" name="Similarity search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
   <description>of small molecules</description>
-  <requirements>
-        <requirement type="package" version="0.1">cheminfolib</requirement>
-  </requirements>
-  <command interpreter="python">
+  <macros>
+    <import>macros.xml</import>
+    <token name="@GALAXY_VERSION@">0</token>
+  </macros>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code">
 <![CDATA[
-    db_similarity_search.py
+    python '$__tool_directory__/db_similarity_search.py'
       --istyle $input_opts.input_style
       #if $input_opts.input_style == 'pattern':
         -i "$input_opts.pattern_string"
@@ -46,65 +48,8 @@
       </when>
     </conditional>
     <param name="tani" type="float" value="0.85" label="Insert the Tanimoto threshold for the query (values range from 0.0 to 1.0)"/>
-    <param name="lib" type="select" label="Select a library of compounds">
-      <options from_file="cheminformatics_chemical_searches_db.loc">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <column name="libname" index="2"/>
-        <column name="db_name" index="3"/>
-        <column name="username" index="4"/>
-        <column name="server" index="5"/>
-        <column name="pswd" index="6"/>
-      </options>
-    </param>
-    <conditional name="output_opts">
-      <param name="output_opts_selector" type="select" label="Select the output format to be printed">
-        <option value="table">Tabular formatted file with molecular properties</option>
-        <option value="can_smiles">Canonical SMILES</option>
-        <option value="inchi">InChI</option>
-        <option value="sdf" selected="True">sdf with molecular properties as meta-data</option>
-        <option value="mol2">mol2</option>
-      </param>
-      <when value="table">
-        <param name="fields" type="select" display="checkboxes" multiple="True" label="Select the attributes to be stored in the generated table file">
-          <option value="can_smiles" selected="True">Canonical SMILES</option>
-          <option value="inchi" selected="False">InChI</option>
-          <option value="inchi_key" selected="False">InChI key</option>
-          <option value="spectrophore" selected="False">Spectrophores(TM) descriptor</option>
-          <option value="molwt" selected="True">Molecular weight</option>
-          <option value="hbd" selected="True">Number of Hydrogen-bond donor groups</option>
-          <option value="hba" selected="True">Number of Hydrogen-bond acceptor groups</option>
-          <option value="rotbonds" selected="True">Number of rotatable bonds</option>
-          <option value="logp" selected="True">Predicted value of LogP</option>
-          <option value="psa" selected="True">Predicted value of the total polar Surface Area of the molecule</option>
-          <option value="mr" selected="False">Predicted value for the Molecular Refractivity</option>
-          <option value="atoms" selected="True">Number of atoms</option>
-          <option value="rings" selected="True">Number of rings</option>
-          <validator type="no_options" message="At least one attribute must be chosen"/>
-        </param>
-        <param name="header" type="boolean" checked="True" label="Print the headers of the table as the first row of the table"/>
-      </when>
-      <when value="can_smiles"/>
-      <when value="inchi"/>
-      <when value="sdf">
-        <param name="fields" type="select" display="checkboxes" multiple="True" label="Select the attributes to be stored in the generated table file">
-          <option value="can_smiles" selected="True">Canonical SMILES</option>
-          <option value="inchi" selected="False">InChI</option>
-          <option value="inchi_key" selected="False">InChI key</option>
-          <option value="spectrophore" selected="False">Spectrophores(TM) descriptor</option>
-          <option value="molwt" selected="True">Molecular weight</option>
-          <option value="hbd" selected="True">Number of Hydrogen-bond donor groups</option>
-          <option value="hba" selected="True">Number of Hydrogen-bond acceptor groups</option>
-          <option value="rotbonds" selected="True">Number of rotatable bonds</option>
-          <option value="logp" selected="True">Predicted value of LogP</option>
-          <option value="psa" selected="True">Predicted value of the total Surface Area of the molecule</option>
-          <option value="mr" selected="False">Predicted value for the Molecular Refractivity</option>
-          <option value="atoms" selected="True">Number of atoms</option>
-          <option value="rings" selected="True">Number of rings</option>
-        </param>
-      </when>
-      <when value="mol2"/>
-    </conditional>
+    <expand macro="lib_param"/>
+    <expand macro="output_opts_param"/>
   </inputs>
     <outputs>
         <data format="sdf" name="outfile">
@@ -117,6 +62,7 @@
         </data>
     </outputs>
     <tests>
+      <test expect_failure="true" />
     </tests>
   <help>
 <![CDATA[
@@ -159,4 +105,5 @@
 
 ]]>
   </help>
+  <expand macro="citations"/>
 </tool>
diff --git a/chemicaltoolbox/pgchem/pgchem/db_substructure_search.xml b/chemicaltoolbox/pgchem/pgchem/db_substructure_search.xml
index f7611bcbc6..e97b026a63 100644
--- a/chemicaltoolbox/pgchem/pgchem/db_substructure_search.xml
+++ b/chemicaltoolbox/pgchem/pgchem/db_substructure_search.xml
@@ -1,11 +1,14 @@
-<tool id="pgchem_db_sub_search" name="Substructure search" version="0.1">
+<tool id="pgchem_db_sub_search" name="Substructure search" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="23.0">
   <description>of small molecules</description>
-  <requirements>
-        <requirement type="package" version="0.1">cheminfolib</requirement>
-  </requirements>
-  <command interpreter="python">
+  <macros>
+    <import>macros.xml</import>
+    <token name="@GALAXY_VERSION@">0</token>
+  </macros>
+  <options sanitize="False"/>
+  <expand macro="requirements"/>
+  <command detect_errors="exit_code">
 <![CDATA[
-    db_substructure_search.py
+    python '$__tool_directory__/db_substructure_search.py'
       --istyle $input_opts.input_style
       #if $input_opts.input_style == 'pattern':
         -i "$input_opts.pattern_string"
@@ -45,63 +48,9 @@
         <param name="pattern_file" type="data" format="smi" label="Select SMILES formatted input file with multiple molecules"/>
       </when>
     </conditional>
-    <param name="lib" type="select" label="Select a library of compounds">
-      <options from_file="cheminformatics_chemical_searches_db.loc">
-        <column name="value" index="0"/>
-        <column name="name" index="1"/>
-        <column name="libname" index="2"/>
-        <column name="db_name" index="3"/>
-        <column name="username" index="4"/>
-        <column name="server" index="5"/>
-        <column name="pswd" index="6"/>
-      </options>
-    </param>
+    <expand macro="lib_param"/>
     <param name="max_results" type="integer" value="500" label="Specify the maximum number of results to be retrieved"/>
-    <conditional name="output_opts">
-      <param name="output_opts_selector" type="select" label="Select the output format to be printed">
-        <option value="table">Tabular formatted file with molecular properties</option>
-        <option value="can_smiles">Canonical SMILES</option>
-        <option value="inchi">InChI</option>
-        <option value="sdf" selected="True">sdf with molecular properties as meta-data</option>
-        <option value="mol2">mol2</option>
-      </param>
-      <when value="table">
-        <param name="fields" type="select" display="checkboxes" multiple="True" label="Select the attributes to be stored in the generated table file">
-          <option value="can_smiles" selected="True">Canonical SMILES</option>
-          <option value="inchi" selected="False">InChI</option>
-          <option value="inchi_key" selected="False">InChI key</option>
-          <option value="spectrophore" selected="False">Spectrophores(TM) descriptor</option>
-          <option value="molwt" selected="True">Molecular weight</option>
-          <option value="hbd" selected="True">Number of Hydrogen-bond donor groups</option>
-          <option value="hba" selected="True">Number of Hydrogen-bond acceptor groups</option>
-          <option value="rotbonds" selected="True">Number of rotatable bonds</option>
-          <option value="logp" selected="True">Predicted value of LogP</option>
-          <option value="psa" selected="True">Predicted value of the total polar Surface Area of the molecule</option>
-          <option value="mr" selected="False">Predicted value for the Molecular Refractivity</option>
-          <option value="atoms" selected="True">Number of atoms</option>
-          <option value="rings" selected="True">Number of rings</option>
-          <validator type="no_options" message="At least one attribute must be chosen"/>
-        </param>
-        <param name="header" type="boolean" checked="True" label="Print the headers of the table as the first row of the table"/>
-      </when>
-      <when value="sdf">
-        <param name="fields" type="select" display="checkboxes" multiple="True" label="Select the attributes to be stored in the generated table file">
-          <option value="can_smiles" selected="True">Canonical SMILES</option>
-          <option value="inchi" selected="False">InChI</option>
-          <option value="inchi_key" selected="False">InChI key</option>
-          <option value="spectrophore" selected="False">Spectrophores(TM) descriptor</option>
-          <option value="molwt" selected="True">Molecular weight</option>
-          <option value="hbd" selected="True">Number of Hydrogen-bond donor groups</option>
-          <option value="hba" selected="True">Number of Hydrogen-bond acceptor groups</option>
-          <option value="rotbonds" selected="True">Number of rotatable bonds</option>
-          <option value="logp" selected="True">Predicted value of LogP</option>
-          <option value="psa" selected="True">Predicted value of the total Surface Area of the molecule</option>
-          <option value="mr" selected="False">Predicted value for the Molecular Refractivity</option>
-          <option value="atoms" selected="True">Number of atoms</option>
-          <option value="rings" selected="True">Number of rings</option>
-        </param>
-      </when>
-    </conditional>
+    <expand macro="output_opts_param"/>
   </inputs>
   <outputs>
     <data name="outfile" format="tabular">
@@ -113,7 +62,9 @@
         </change_format>
     </data>
   </outputs>
-  <options sanitize="False"/>
+  <tests>
+    <test expect_failure="true" />
+  </tests>
   <help>
 <![CDATA[
 
@@ -155,4 +106,5 @@
 
 ]]>
   </help>
+  <expand macro="citations"/>
 </tool>
diff --git a/chemicaltoolbox/pgchem/pgchem/macros.xml b/chemicaltoolbox/pgchem/pgchem/macros.xml
new file mode 100644
index 0000000000..ebabafca52
--- /dev/null
+++ b/chemicaltoolbox/pgchem/pgchem/macros.xml
@@ -0,0 +1,79 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">cheminfolib</requirement>
+        </requirements>
+    </xml>
+    <xml name="lib_param">
+        <param name="lib" type="select" label="Select a library of compounds">
+            <options from_data_table="cheminformatics_chemical_searches_db.loc">
+              <column name="value" index="0"/>
+              <column name="name" index="1"/>
+              <column name="libname" index="2"/>
+              <column name="db_name" index="3"/>
+              <column name="username" index="4"/>
+              <column name="server" index="5"/>
+              <column name="pswd" index="6"/>
+            </options>
+          </param>
+    </xml>
+
+    <xml name="output_opts_param">
+        <conditional name="output_opts">
+            <param name="output_opts_selector" type="select" label="Select the output format to be printed">
+              <option value="table">Tabular formatted file with molecular properties</option>
+              <option value="can_smiles">Canonical SMILES</option>
+              <option value="inchi">InChI</option>
+              <option value="sdf" selected="True">sdf with molecular properties as meta-data</option>
+              <option value="mol2">mol2</option>
+            </param>
+            <when value="table">
+              <param name="fields" type="select" display="checkboxes" multiple="True" label="Select the attributes to be stored in the generated table file">
+                <option value="can_smiles" selected="True">Canonical SMILES</option>
+                <option value="inchi" selected="False">InChI</option>
+                <option value="inchi_key" selected="False">InChI key</option>
+                <option value="spectrophore" selected="False">Spectrophores(TM) descriptor</option>
+                <option value="molwt" selected="True">Molecular weight</option>
+                <option value="hbd" selected="True">Number of Hydrogen-bond donor groups</option>
+                <option value="hba" selected="True">Number of Hydrogen-bond acceptor groups</option>
+                <option value="rotbonds" selected="True">Number of rotatable bonds</option>
+                <option value="logp" selected="True">Predicted value of LogP</option>
+                <option value="psa" selected="True">Predicted value of the total polar Surface Area of the molecule</option>
+                <option value="mr" selected="False">Predicted value for the Molecular Refractivity</option>
+                <option value="atoms" selected="True">Number of atoms</option>
+                <option value="rings" selected="True">Number of rings</option>
+                <validator type="no_options" message="At least one attribute must be chosen"/>
+              </param>
+              <param name="header" type="boolean" checked="True" label="Print the headers of the table as the first row of the table"/>
+            </when>
+            <when value="can_smiles"/>
+            <when value="inchi"/>
+            <when value="sdf">
+              <param name="fields" type="select" display="checkboxes" multiple="True" label="Select the attributes to be stored in the generated table file">
+                <option value="can_smiles" selected="True">Canonical SMILES</option>
+                <option value="inchi" selected="False">InChI</option>
+                <option value="inchi_key" selected="False">InChI key</option>
+                <option value="spectrophore" selected="False">Spectrophores(TM) descriptor</option>
+                <option value="molwt" selected="True">Molecular weight</option>
+                <option value="hbd" selected="True">Number of Hydrogen-bond donor groups</option>
+                <option value="hba" selected="True">Number of Hydrogen-bond acceptor groups</option>
+                <option value="rotbonds" selected="True">Number of rotatable bonds</option>
+                <option value="logp" selected="True">Predicted value of LogP</option>
+                <option value="psa" selected="True">Predicted value of the total Surface Area of the molecule</option>
+                <option value="mr" selected="False">Predicted value for the Molecular Refractivity</option>
+                <option value="atoms" selected="True">Number of atoms</option>
+                <option value="rings" selected="True">Number of rings</option>
+              </param>
+            </when>
+            <when value="mol2"/>
+        </conditional>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/1758-2946-3-33</citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>
\ No newline at end of file
diff --git a/chemicaltoolbox/simsearch/simsearch.xml b/chemicaltoolbox/simsearch/simsearch.xml
index 2d03608ed9..744efa2202 100644
--- a/chemicaltoolbox/simsearch/simsearch.xml
+++ b/chemicaltoolbox/simsearch/simsearch.xml
@@ -2,7 +2,7 @@
     <description>of fingerprint data sets with chemfp</description>
     <macros>
         <token name="@TOOL_VERSION@">1.6.1</token>
-        <token name="@GALAXY_VERSION@">0</token>
+        <token name="@GALAXY_VERSION@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">chemfp</requirement>
@@ -97,8 +97,8 @@
         <test>
             <param name="targets" ftype="fps" value="targets.fps"/>
             <param name="query" ftype="fps" value="q.fps"/>
-            <param name="k" value='4'/>
-            <param name="th" value='0.7'/>
+            <param name="knn" value='4'/>
+            <param name="threshold" value='0.7'/>
             <output name="outfile" ftype="tabular" file="simsearch_on_tragets_and_q.tabular"/>
         </test>
     </tests>
@@ -113,7 +113,7 @@
 Similarity searches using a variety of different fingerprints using either the chemfp_ FPS type or the Open Babel FastSearch_ index.
 
 .. _chemfp: http://chemfp.com/
-.. _FastSearch: http://openbabel.org/wiki/FastSearch
+.. _FastSearch: https://open-babel.readthedocs.io/en/latest/Command-line_tools/babel.html#substructure-and-similarity-searching
 
 
 ]]>
diff --git a/chemicaltoolbox/simsearch/test-data/simsearch_on_tragets_and_q.tabular b/chemicaltoolbox/simsearch/test-data/simsearch_on_tragets_and_q.tabular
index 8eb3a22cf5..6c31956ec4 100644
--- a/chemicaltoolbox/simsearch/test-data/simsearch_on_tragets_and_q.tabular
+++ b/chemicaltoolbox/simsearch/test-data/simsearch_on_tragets_and_q.tabular
@@ -1,9 +1,9 @@
 #Simsearch/1
 #num_bits=881
-#type=Tanimoto k=all threshold=0.7
+#type=Tanimoto k=4 threshold=0.7
 #software=chemfp/1.6.1
 #queries=./query.fps
 #targets=./targets.fps
 #query_source=CID_28434379.sdf
 #target_source=Desktop/3579363516810334491.sdf
-13	28434379	6499094	0.9615	6485578	0.9679	55079807	0.9313	3153534	0.9557	55102353	0.9682	55091466	0.9682	55091416	0.9682	6485577	0.9497	55169009	0.9560	55091752	0.9684	55091467	0.9623	55168823	0.9563	55091849	0.9563
+4	28434379	55091752	0.9684	55102353	0.9682	55091466	0.9682	55091416	0.9682
diff --git a/chemicaltoolbox/xchem-deep/.shed.yml b/chemicaltoolbox/xchem-deep/.shed.yml
new file mode 100644
index 0000000000..59480cf115
--- /dev/null
+++ b/chemicaltoolbox/xchem-deep/.shed.yml
@@ -0,0 +1,12 @@
+name: xchem_transfs_scoring
+owner: bgruening
+remote_repository_url: "https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/xchem-deep"
+homepage_url: "https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/xchem-deep"
+categories:
+- Computational chemistry
+description: "This tool performs scoring of docked ligand poses using deep learning."
+long_description: |
+  This tool performs scoring of docked ligand poses using deep learning.
+  It uses the gnina and libmolgrid toolkits to perform the scoring to generate
+  a prediction for how good the pose is.
+type: unrestricted
\ No newline at end of file
diff --git a/chemicaltoolbox/xchem-deep/transfs.xml b/chemicaltoolbox/xchem-deep/transfs.xml
index ca09832e36..fe753789b6 100644
--- a/chemicaltoolbox/xchem-deep/transfs.xml
+++ b/chemicaltoolbox/xchem-deep/transfs.xml
@@ -1,4 +1,4 @@
-<tool id="xchem_transfs_scoring" name="XChem TransFS pose scoring" version="0.4.0">
+<tool id="xchem_transfs_scoring" name="XChem TransFS pose scoring" version="1.3+galaxy0" profile="23.0">
     <description>using deep learning</description>
 
     <requirements>
@@ -66,8 +66,7 @@
                     <has_text text="TransFSReceptor"/>
                     <has_text text="TransFSScore"/>
                 </assert_contents>
-            </output> -->
-            <!---output_collection name="pdb_files" type="list" count="2" /-->
+            </output>
         </test>
         <test>
             <param name="receptor" value="receptor.pdb"/>
@@ -134,4 +133,7 @@ examined against input PDB structure and the with waters that clash (any heavy a
 the 'distance' parameter being removed. The file names are encoded with the water numbers that are removed.
 
     ]]></help>
+    <citations>
+        <citation type="doi">10.1186/s13321-020-00442-7</citation>
+    </citations>
 </tool>