--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/constrained_conf_gen.xml	Tue Jul 21 05:25:31 2020 -0400
@@ -0,0 +1,73 @@
+<tool id="ctb_im_constrained_conf_gen" name="Constrained conformer generation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
+    <description>with RDKit</description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@GALAXY_VERSION@">0</token>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s $refmol ./refmol.sdf &&
+        python -m pipelines.rdkit.constrained_conf_gen
+            -i '$infile'
+            -if sdf
+            -r './refmol.sdf'
+            #if $core_smi
+                -c '$core_smi'
+            #end if
+            -n $number
+            --refmolidx $refmolidx
+            --meta
+            -o outp
+            -of sdf &>> $logfile &&
+        cat outp_metrics.txt &>> $logfile &&
+        gzip -dc outp.sdf.gz &>> outp.sdf || :
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
+        <param name="refmol" type="data" format="sdf" label="SDF reference file" help="ABCD"/>
+        <param name="refmolidx" type="integer" value="1" label="Reference molecule index" help="Index of the reference molecule index in the file, if not the first"/>
+        <param name="number" type="integer" value="10" label="Number of conformers" help="Number of conformers to generate, if None then input structures are assumed to already be 3D')"/>
+        <param name="core_smi" type="text" value="" label="Core substructure" help="If not specified - guessed using MCS"/>
+    </inputs>
+    
+    <expand macro="outputs" />
+
+    <tests>
+        <test>
+            <param name="infile" value="XChemReactionMaker1.sdf" ftype="sdf"/>
+            <param name="refmol" value="ref_mol.sdf" ftype="sdf"/>
+            <param name="number" value="2" />
+            <output name="outfile" ftype="sdf" file="constrained_conf_gen_output1.sdf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+This tool generates constrained conformers for a set of input molecules, using the chemistry toolkit RDKit.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+| - Molecules in `SDF format`_
+| - Reference molecule in SDF format.
+
+.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
+
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+SD-file containing generated conformers.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>