--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cml_to_smi_converter.xml	Thu Aug 15 03:19:26 2013 -0400
@@ -0,0 +1,42 @@
+<tool id="CONVERTER_cml_to_smiles" name="CML to SMILES" version="1.0.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command >
+        obabel -icml "${input}"
+        #if $can:
+            -ocan
+        #else:
+            -osmi 
+        #end if
+            -O "${output}" -e 
+        $remove_h
+        #if $iso_chi or $can or $exp_h:
+            -x$iso_chi$exp_h$can
+        #end if
+        #if $dative_bonds:
+            -b
+        #end if
+        #if int($ph) >= 0:
+            -p $ph
+        #end if
+
+        2>&#38;1
+    </command>
+    <inputs>
+        <param name="input" type="data" format="cml" label="Molecules in CML-format"/>
+        <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" />
+        <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" />
+        <param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" />
+        <param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" />
+        <param name="ph" size="3" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/>
+        <param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" />
+    </inputs>
+    <outputs>
+        <data name="output" format="smi"/>
+    </outputs>
+    <help>
+    </help>
+</tool>