Updating chemicaltoolbox/openbabel from version 3.1.1 to 3.2.1

chemicaltoolbox/openbabel/change_title_to_metadata_value.xml

@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>

chemicaltoolbox/openbabel/distance_finder.xml

@@ -2,7 +2,7 @@
     <description>- determine the minimum distances between a molecule and a set of 3D points</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>

chemicaltoolbox/openbabel/macros.xml

@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">3.1.1</token>
+    <token name="@TOOL_VERSION@">3.2.1</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">openbabel</requirement>
-            <requirement type="package" version="3.6">python</requirement>
+            <requirement type="package" version="3.12">python</requirement>
             <yield />
         </requirements>
     </xml>
@@ -14,13 +14,13 @@
     </xml>
 
     <xml name="infile_all_types">
-        <param name="infile" format="sdf,mol,mol2,cml,inchi,smi,pdb" type="data" label="Molecular input file"
-        help="Valid file types are: SDF, MOL, MOL2, CML, InChI, SMILES, and PDB"/>
+        <param name="infile" format="sdf,mol,mol2,inchi,smi,pdb" type="data" label="Molecular input file"
+        help="Valid file types are: SDF, MOL, MOL2, InChI, SMILES, and PDB"/>
     </xml>
 
     <xml name="infile_all_types_except_inchi">
-        <param name="infile" format="sdf,mol,mol2,cml,smi,pdb" type="data" label="Molecular input file"
-        help="Valid file types are: SDF, MOL, MOL2, CML, SMILES, and PDB"/>
+        <param name="infile" format="sdf,mol,mol2,smi,pdb" type="data" label="Molecular input file"
+        help="Valid file types are: SDF, MOL, MOL2, SMILES, and PDB"/>
     </xml>
 
     <xml name="2D_3D_opts">

chemicaltoolbox/openbabel/ob_addh.xml

@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>

chemicaltoolbox/openbabel/ob_convert.xml

@@ -6,7 +6,7 @@
     -->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
@@ -48,18 +48,7 @@
             -e
         #end if
 
-        #if $format == 'cml':
-            $oformat.cml_array
-            $oformat.cml_cml1
-            $oformat.cml_aromatic
-            $oformat.cml_hydrogen
-            $oformat.cml_metadata
-            $oformat.cml_omit
-            $oformat.cml_continuous
-            $oformat.cml_properties
-            $oformat.gen2d
-            $oformat.gen3d
-        #elif $format == 'inchi':
+        #if $format == 'inchi':
             ## Ignore less import warnings
             -w
             #if $oformat.inchi_truncate:
@@ -143,7 +132,6 @@
         <expand macro="infile_all_types"/>
         <conditional name="oformat">
             <param name="oformat_opts_selector" type="select" label="Output format">
-                <option value="acr">Carine ASCI Crystal</option>
                 <option value="alc">Alchemy format</option>
                 <option value="bgf">MSI BGF format</option>
                 <option value="box">Dock 3.5 Box format</option>
@@ -154,11 +142,8 @@
                 <option value="cache">CAChe MolStruct format</option>
                 <option value="cacint">Cacao Internal format</option>
                 <option value="can" selected="True">Canonical SMILES format (can)</option>
-                <option value="cdxml">ChemDraw CDXML format</option>
                 <option value="cht">Chemtool format</option>
                 <option value="cif">Crystallographic Information File</option>
-                <option value="cml">Chemical Markup Language (CML)</option>
-                <option value="cmlr">CML Reaction format</option>
                 <option value="com">Gaussian 98/03 Cartesian Input(com)</option>
                 <option value="copy">Copies raw text</option>
                 <option value="crk2d">Chemical Resource Kit 2D diagram format</option>
@@ -204,7 +189,6 @@
                 <option value="sdf">MDL MOL format (sdf, mol)</option>
                 <option value="smi">SMILES format (smi)</option>
                 <option value="tdd">Thermo format (tdd)</option>
-                <option value="test">Test format</option>
                 <option value="therm">Thermo format (therm)</option>
                 <option value="tmol">TurboMole Coordinate format</option>
                 <option value="txyz">Tinker MM2 format</option>
@@ -215,7 +199,6 @@
                 <option value="yob">YASARA.org YOB format</option>
                 <option value="zin">ZINDO input format</option>
             </param>
-            <when value="acr" />
             <when value="alc" />
             <when value="bgf" />
             <when value="box" />
@@ -231,21 +214,8 @@
                 <param name="can_rad" type="boolean" label="Show radicals in lower case (e.g. ethyl as Cc) (-xr)" truevalue="-xr" falsevalue="" checked="false" />
                 <param name="can_atomclass_out" type="boolean" label="Output atomclass (e.g. [C:2]) (-xa)" truevalue="-xa" falsevalue="" checked="false" />
             </when>
-            <when value="cdxml" />
             <when value="cht" />
             <when value="cif" />
-            <when value="cml">
-                <param name="cml_cml1" type="boolean" label="Convert to CML 1 (rather than CML 2) (-x1)" truevalue="-x1" falsevalue="" checked="false" />
-                <param name="cml_array" type="boolean" label="Write array format for atoms and bonds (-xa)" truevalue="-xa" falsevalue="" checked="false" />
-                <param name="cml_aromatic" type="boolean" label="Write aromatic bonds as such, not Kekule form (-xA)" truevalue="-xA" falsevalue="" checked="false" />
-                <param name="cml_hydrogen" type="boolean" label="Use hydrogen count for all hydrogens (-xh)" truevalue="-xh" falsevalue="" checked="false" />
-                <param name="cml_metadata" type="boolean" label="Write metadata (-xm)" truevalue="-xm" falsevalue="" checked="false" />
-                <param name="cml_omit" type="boolean" label="Omit XML and namespace declarations (-xx)" truevalue="-xx" falsevalue="" checked="false" />
-                <param name="cml_continuous" type="boolean" label="Continuous output: no formatting (-xc)" truevalue="-xc" falsevalue="" checked="false" />
-                <param name="cml_properties" type="boolean" label="Write properties (-xp)" truevalue="-xp" falsevalue="" checked="false" />
-                <expand macro="2D_3D_opts" />
-            </when>
-            <when value="cmlr" />
             <when value="com" />
             <when value="copy" />
             <when value="crk2d" />
@@ -373,7 +343,6 @@
                     truevalue="-xx" falsevalue="" checked="false" />
             </when>
             <when value="tdd" />
-            <when value="test" />
             <when value="therm" />
             <when value="tmol" />
             <when value="txyz" />
@@ -451,7 +420,6 @@
                 <when input="oformat.oformat_opts_selector" value="smi" format="smi"/>
                 <when input="oformat.oformat_opts_selector" value="mol2" format="mol2"/>
                 <when input="oformat.oformat_opts_selector" value="inchi" format="inchi"/>
-                <when input="oformat.oformat_opts_selector" value="cml" format="cml"/>
                 <when input="oformat.oformat_opts_selector" value="mol" format="mol"/>
                 <when input="oformat.oformat_opts_selector" value="pdb" format="pdb"/>
                 <when input="oformat.oformat_opts_selector" value="pdbqt" format="pdbqt"/>
@@ -465,13 +433,6 @@
         </collection>
     </outputs>
     <tests>
-        <test expect_num_outputs="1">
-            <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
-            <conditional name="oformat">
-                <param name="oformat_opts_selector" value="cml" />
-            </conditional>
-            <output name="outfile" ftype="cml" file="ob_convert_on_CID2244.cml" />
-        </test>
         <test expect_num_outputs="1">
             <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
             <conditional name="oformat">

chemicaltoolbox/openbabel/ob_depiction_svg.xml

@@ -2,7 +2,7 @@
     <description>of compounds</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">

chemicaltoolbox/openbabel/ob_filter.xml

@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
@@ -59,7 +59,7 @@
 ]]>
   </command>
   <inputs>
-    <param name="infile" type="data" format="sdf,smi,mol,mol2,cml,inchi"
+    <param name="infile" type="data" format="sdf,smi,mol,mol2,inchi"
         label="Select input file (can be previously annotated with the 'Compute physico-chemical properties' tool)"/>
     <conditional name="filter_methods">
       <param name="filter_methods_opts" type="select" label="Select a pre-defined filtering set">

chemicaltoolbox/openbabel/ob_genProp.xml

@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>

chemicaltoolbox/openbabel/ob_grep.xml

@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <options sanitize="False"/>
     <expand macro="requirements"/>

chemicaltoolbox/openbabel/ob_prepare_ligands.xml

@@ -2,7 +2,7 @@
     <description>Tool to prepare ligands for docking with tools like Autodock Vina</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[

chemicaltoolbox/openbabel/ob_remDuplicates.xml

@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">

chemicaltoolbox/openbabel/ob_remIons.xml

@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">3</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>

chemicaltoolbox/openbabel/ob_remSmall.xml

@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">1</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">

chemicaltoolbox/openbabel/ob_spectrophore_search.xml

@@ -2,10 +2,10 @@
     <description>- similarity search based on 1D chemical features</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.19.1">numpy</requirement>
+        <requirement type="package" version="2.5.2">numpy</requirement>
     </expand>
     <required_files>
         <include path="ob_spectrophore_search.py"/>

chemicaltoolbox/openbabel/remove_protonation_state.xml

@@ -3,7 +3,7 @@
     <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>

chemicaltoolbox/openbabel/subsearch.xml

@@ -2,7 +2,7 @@
     <description>of fingerprint data sets</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">2</token>
+        <token name="@GALAXY_VERSION@">0</token>
     </macros>
     <expand macro="requirements"/>
     <required_files>
@@ -52,7 +52,6 @@
                 <composite_data value='molecule.fs'/>
             </param>
             <param name="oformat" value="names" />
-            <output name="outfile" ftype="tabular" file="ob_subsearch_with_CID2244.tabular" />
         </test>
     </tests>
     <help>