--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sdf_to_tab.xml	Wed Oct 16 07:26:19 2019 -0400
@@ -0,0 +1,113 @@
+<tool id="sdf_to_tab" name="Extract values from an SD-file" version="@VERSION@">
+    <macros>
+        <token name="@VERSION@">2019.03.1</token>
+    </macros>
+    <description>into a tabular file using RDKit</description>
+    <requirements>
+        <requirement type="package" version="@VERSION@">rdkit</requirement>        
+    </requirements>
+    <command detect_errors="exit_code">
+<![CDATA[
+        python '$__tool_directory__/sdf_to_tab.py'
+            -i '${infile}'
+            -o '${outfile}'
+            -p '$props'
+            $header
+            $smiles
+            $name
+]]>
+    </command>
+    <inputs>
+        <param name="infile" format="sdf" type="data" label="Input SD-file"/>
+        <param name="header" type="boolean" label="Include the property name as header"
+            truevalue="--header" falsevalue="" checked="false" />
+        <param name="smiles" type="boolean" label="Include SMILES as column in output"
+            truevalue="--smiles" falsevalue="" checked="false" />
+        <param name="name" type="boolean" label="Include molecule name as column in output"
+            truevalue="--name" falsevalue="" checked="false" />
+        <param name="props" type="text" optional="true" label="Properties to extract from the SD-file" help="Separated with a comma, e.g. RMSD_UB,RMSD_LB,SCORE. To extract values for all properties in the file, leave the field blank."/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype='sdf' value="CID_3037.sdf" />
+            <param name="header" value="True" />
+            <param name="props" value="" />
+            <param name="name" value="True" />
+            <output name="outfile" ftype='tabular' file="CID_3037.tab" />
+
+        </test>
+        <test>
+            <param name="infile" ftype='sdf' value="ligand.sdf" />
+            <param name="header" value="True" />
+            <param name="props" value="RMSD_UB,RMSD_LB,SCORE" />
+            <param name="smiles" value="True" />
+            <output name="outfile" ftype='tabular' file="ligand.tab" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Structure-data (SD-) files may contain values for various properties saved under each of the records. These are indicated using angled brackets, as in the following extract::
+
+    >  <TORSDO>
+    F 3
+
+    >  <SCORE>
+    -4.9
+
+    >  <RMSD_LB>
+    0.000
+
+    >  <RMSD_UB>
+    0.000
+
+This tool extracts properties for all molecules saved within an input SD-file, using RDKit, and saves them to tabular format.
+
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+An SD-file. The properties to be extracted can also be specified, separated with a comma; for example, SCORE,RMSD_LB,RMSD_UB.
+
+If the field is left blank, all properties found in the SD-file will be saved, excluding properties with values that contain newline or tab characters, which would disrupt the tabular format.
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+Tabular file, where each property is shown in a separate column, with compounds found in the SD-file listed in each row::
+
+    Name    RMSD_LB RMSD_UB SCORE
+    pose1   0.0     0.0     -4.9
+    pose2   0.118   2.246   -4.9
+    pose3   2.96    5.795   -4.9
+    pose4   2.958   5.379   -4.8
+    pose5   2.763   5.379   -4.5
+    pose6   3.106   4.85    -4.4
+    pose7   2.847   5.816   -4.4
+    pose8   3.964   5.892   -4.3
+    pose9   3.971   6.363   -4.3
+
+]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @article{rdkit,
+                author = {Greg Landrum and others},
+                title = {RDKit: Open-source cheminformatics},
+                url ={http://www.rdkit.org}
+            }</citation>
+    </citations>
+</tool>