--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/o3dalign.xml	Tue Jul 21 05:24:46 2020 -0400
@@ -0,0 +1,103 @@
+<tool id="ctb_im_o3dalign" name="Open 3D Align" 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 $molquery ./molquery.sdf &&
+        o3dAlign
+            ./molquery.sdf  ##positional arg
+            -i '$infile'
+            -if sdf
+            --qmolidx '$qmolidx'
+            $crippen
+            -n '$number'
+            -t '$threshold'
+            -a '$attempts'
+            -r '$rmsd'
+            -e '$emin'
+            --meta
+            -of sdf
+            -o outp &>> $logfile &&
+        cat outp_metrics.txt &>> $logfile &&
+        gzip -d outp.sdf.gz
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
+        <param name="molquery" type="data" format="sdf,mol" label="Mol query file" help="Mol file to align against"/>
+        <param name="qmolidx" type="integer" value="1" label="Query molecule index" help="Query molecule index in SD-file if not the first"/>
+        <param name="threshold" type="float" min="0" value="1" label="Threshold" help="Score cutoff relative to alignment of query to itself"/>
+        <param name="number" type="integer" value="0" label="Number of conformers" help="Number of conformers to generate, if 0 then input structures are assumed to already be)"/>
+        <param name="rmsd" type="float" min="0" value="1.0" label="RMSD Threshold" help="Prune RMSD threshold for excluding conformers"/>
+        <param name="attempts" type="integer" min="0" value="0" label="Number of attempts" help="If confomers fall below the RMSD threshold, number of attempts at regeneration before giving up."/>
+        <param name="emin" type="integer" value="0" label="Energy minimisation iterations" help="Number of EM iterations using the MMFF force field. Default is 0 (i.e. no EM)."/>
+        <param name="crippen" type="boolean" label="Crippen" truevalue="--crippen" falsevalue="" help="Use Crippen (logP) contributions"/>
+    </inputs>
+    
+    <expand macro="outputs" />
+    
+    <tests>
+        <test>
+            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
+            <param name="molquery" value="pyrimethamine.mol" ftype="mol"/>
+            <param name="threshold" value="30" />
+            <param name="number" value="2" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1"/>
+                </assert_contents>
+            </output>
+            <output name="logfile">
+                <assert_contents>
+                    <has_text text="Perfect score: 0.0 134.34 CCc1nc(N)nc(N)c1-c1ccc(Cl)cc1 17"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
+            <param name="molquery" value="pyrimethamine.mol" ftype="mol"/>
+            <param name="threshold" value="30" />
+            <param name="number" value="2" />
+            <param name="crippen" value="--crippen" />
+            <output name="outfile">
+                <assert_contents>
+                    <has_text text="Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1"/>
+                </assert_contents>
+            </output>
+            <output name="logfile">
+                <assert_contents>
+                    <has_text text="Perfect score: 0.0 114.13359999999997 CCc1nc(N)nc(N)c1-c1ccc(Cl)cc1 17"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Aligns molecules using RDKit's Open 3D Align.
+
+.. class:: infomark
+
+**Input**
+
+| - Input file in `SDF Format`_
+
+.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+SD-file of aligned compounds.
+
+]]></help>
+    <expand macro="citations" />
+</tool>
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