diff ob_convert.xml @ 16:b1dda415eecd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf

--- a/ob_convert.xml	Tue Nov 10 20:21:08 2020 +0000
+++ b/ob_convert.xml	Thu Aug 15 10:59:50 2024 +0000
@@ -6,7 +6,7 @@
     -->
     <macros>
         <import>macros.xml</import>
-        <token name="@GALAXY_VERSION@">0</token>
+        <token name="@GALAXY_VERSION@">1</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="aggressive">
@@ -132,7 +132,11 @@
         #if float($ph) >= 0:
             -p $ph
         #end if
-
+        
+        #if $appendproperties:
+            #set $props = str($appendproperties).replace(',', ' ')
+            --append '$props'
+        #end if
 ]]>
     </command>
     <inputs>
@@ -155,7 +159,7 @@
                 <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</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>
                 <option value="crk3d">Chemical Resource Kit 3D format</option>
@@ -163,8 +167,6 @@
                 <option value="cssr">CSD CSSR format</option>
                 <option value="ct">ChemDraw Connection Table format</option>
                 <option value="dmol">DMol3 coordinates format</option>
-                <!--<option value="ent">Protein Data Bank format</option>
-                <option value="fa">FASTA format</option>-->
                 <option value="fasta">FASTA format</option>
                 <option value="feat">Feature format</option>
                 <option value="fh">Fenske-Hall Z-Matrix format</option>
@@ -172,27 +174,22 @@
                 <option value="fpt">Fingerprint format (fpt)</option>
                 <option value="fract">Free Form Fractional format</option>
                 <option value="fs">Open Babel FastSearching database (fs)</option>
-                <!--<option value="fsa">FASTA format</option>-->
-                <option value="gamin">GAMESS Input</option>
-                <option value="gau">Gaussian 98/03 Cartesian Input</option>
-                <!--<option value="gjc">Gaussian 98/03 Cartesian Input</option>
-                <option value="gjf">Gaussian 98/03 Cartesian Input</option>-->
+                <option value="gamin">GAMESS Input (gamin)</option>
+                <option value="inp">GAMESS Input (inp)</option>
+                <option value="gau">Gaussian 98/03 Cartesian Input(gau)</option>
                 <option value="gpr">Ghemical format</option>
                 <option value="gr96">GROMOS96 format</option>
                 <option value="hin">HyperChem HIN format</option>
                 <option value="inchi">IUPAC InChI</option>
-                <option value="inp">GAMESS Input</option>
                 <option value="jin">Jaguar input format</option>
-                <!--<option value="mdl">MDL MOL format (mol)</option>-->
-                <option value="mmd">MacroModel format</option>
-                <option value="mmod">MacroModel format</option>
-                <!--<option value="mol">MDL MOL format (mol)</option> use SDF-->
+                <option value="mmd">MacroModel format (mmd)</option>
+                <option value="mmod">MacroModel format (mmod)</option>
                 <option value="mol2">Sybyl Mol2 format (mol2)</option>
                 <option value="molreport">Open Babel molecule report</option>
-                <option value="mop">MOPAC Cartesian format</option>
-                <option value="mopcrt">MOPAC Cartesian format</option>
+                <option value="mop">MOPAC Cartesian format (mop)</option>
+                <option value="mopcrt">MOPAC Cartesian format (mopcrt)</option>
                 <option value="mopin">MOPAC Internal</option>
-                <option value="mpc">MOPAC Cartesian format</option>
+                <option value="mpc">MOPAC Cartesian format (mpc)</option>
                 <option value="mpd">Sybyl descriptor format</option>
                 <option value="mpqcin">MPQC simplified input format</option>
                 <option value="nw">NWChem input format</option>
@@ -204,13 +201,11 @@
                 <option value="qcin">Q-Chem input format</option>
                 <option value="report">Open Babel report format</option>
                 <option value="rxn">MDL RXN format</option>
-                <!--<option value="sd">MDL MOL format</option>-->
                 <option value="sdf">MDL MOL format (sdf, mol)</option>
                 <option value="smi">SMILES format (smi)</option>
-                <!--<option value="sy2">Sybyl Mol2 format</option>-->
-                <option value="tdd">Thermo format</option>
+                <option value="tdd">Thermo format (tdd)</option>
                 <option value="test">Test format</option>
-                <option value="therm">Thermo format</option>
+                <option value="therm">Thermo format (therm)</option>
                 <option value="tmol">TurboMole Coordinate format</option>
                 <option value="txyz">Tinker MM2 format</option>
                 <option value="unixyz">UniChem XYZ format</option>
@@ -398,6 +393,27 @@
         <param name="dative_bonds" type="boolean" truevalue="-b" falsevalue=""
             label="Convert dative bonds" help="e.g. [N+]([O-])=O to N(=O)=O (-b)" />
         <param name="appendtotitle" type="text" value="" label="Append the specified text after each molecule title"/>
+        <param name="appendproperties" type="select" multiple="true" label="Molecular properties to append to the title." optional="true">
+            <option value="abonds">Number of aromatic bonds</option>
+            <option value="atoms">Number of atoms</option>
+            <option value="bonds">Number of bonds</option>
+            <option value="cansmi">Canonical SMILES</option>
+            <option value="cansmiNS">Canonical SMILES without isotopes or stereo</option>
+            <option value="dbonds">Number of double bonds</option>
+            <option value="sbonds">Number of single bonds</option>
+            <option value="tbonds">Number of triple bonds</option>
+            <option value="formula">Chemical formula</option>
+            <option value="HBA1">Number of Hydrogen Bond Acceptors 1 (JoelLib)</option>
+            <option value="HBA2">Number of Hydrogen Bond Acceptors 2 (JoelLib)</option>
+            <option value="HBD">Number of Hydrogen Bond Donors (JoelLib)</option>
+            <option value="InChI">IUPAC InChI identifier</option>
+            <option value="InChIKey">InChIKey</option>
+            <option value="L5">Lipinski Rule of Five</option>
+            <option value="logP">octanol/water partition coefficient</option>
+            <option value="MR">molar refractivity</option>
+            <option value="MW">Molecular Weight</option>
+            <option value="TPSA">topological polar surface area</option>
+        </param>
 
         <!-- Uniqueness -->
         <conditional name="unique">
@@ -449,40 +465,40 @@
         </collection>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
             <param name="oformat_opts_selector" value="cml" />
             <output name="outfile" ftype="cml" file="ob_convert_on_CID2244.cml" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
             <param name="oformat_opts_selector" value="fs" />
-            <output name="outfile" compare="contains" file="ob_convert_on_CID2244_obfs.txt" ftype="obfs">
+            <output name="outfile" compare="contains" file="ob_convert_on_CID2244_obfs.txt" ftype="obfs" >
                 <extra_files type="file" value="molecule.sdf" name="molecule.sdf" />
                 <extra_files type="file" value="molecule.fs" name="molecule.fs" compare="sim_size" />
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
             <param name="oformat_opts_selector" value="inchi" />
             <output name="outfile" ftype="inchi" file="ob_convert_on_CID2244.inchi" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
             <param name="oformat_opts_selector" value="pdb" />
             <output name="outfile" ftype="pdb" file="ob_convert_on_CID2244.pdb" lines_diff="4" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
             <param name="oformat_opts_selector" value="can" />
             <output name="outfile" ftype="smi" file="ob_convert_on_CID2244.smi" />
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" ftype="sdf" value="CID_2244.sdf"/>
             <param name="oformat_opts_selector" value="sdf" />
             <output name="outfile" ftype="sdf" file="ob_convert_on_CID2244.sdf" lines_diff="2"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="infile" ftype="smi" value="2_mol.smi"/>
             <param name="oformat_opts_selector" value="pdbqt"/>
             <param name="split" value="true"/>
@@ -491,6 +507,12 @@
                 <element name="molecule2" file="split2.pdbqt" />
             </output_collection>
         </test>
+        <test expect_num_outputs="1">
+            <param name="infile" ftype="smi" value="2_mol.smi"/>
+            <param name="oformat_opts_selector" value="sdf" />
+            <param name="appendproperties" value="cansmi,InChI"/>
+            <output name="outfile" ftype="sdf" file="2_mol.sdf" lines_diff="4"/>
+        </test>
     </tests>
     <help>
 <![CDATA[