--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/enumerate_charges.xml	Tue Mar 10 12:57:24 2020 -0400
@@ -0,0 +1,98 @@
+<tool id="enumerate_charges" name="Enumerate changes" version="0.1">
+    <description>calculated with Dimorphite DL and RDKit</description>
+      <requirements>
+        <requirement type="package" version="2019.09.2">rdkit</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+<![CDATA[
+        python '$__tool_directory__/dimorphite_dl.py'
+            --smiles_file '$input'
+            --output_file '$output'
+            --min_ph $min_ph
+            --max_ph $max_ph
+]]>
+    </command>
+    <inputs>
+        <param name="input" format="smi" type="data" label="Input molecule data"
+            help="In SMILES format"/>
+        <param name="min_ph" type="float" label="Minimum pH" value="6.4" min="0" max="14"/>
+        <param name="max_ph" type="float" label="Maximum pH" value="8.4" min="0" max="14"/>
+    </inputs>
+    <outputs>
+        <data format="smi" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype='smi' value="mols.smi" />
+            <param name="min_ph"  value="6.4" />
+            <param name="max_ph"  value="8.4" />
+            <output name="output" ftype='smi'>
+                <!-- there are problems comparing the output to the expected due to whitespace differences
+                so we just check that the number of lines is as expected -->
+                <assert_contents>
+                    <has_n_lines n="7" />
+                    <has_text text="NC(CCCC[NH3+])C(=O)[O-]" />
+                    <has_text text="NCCCCC(N)C(=O)[O-]" />
+                    <has_text text="NCCCCC([NH3+])C(=O)[O-]" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" ftype='smi' value="mols.smi" />
+            <param name="min_ph"  value="4.4" />
+            <param name="max_ph"  value="10.4" />
+            <output name="output" ftype='smi'>
+                <assert_contents>
+                    <has_n_lines n="14" />
+                    <has_text text="NC(CCCC[NH3+])C(=O)O" />
+                    <has_text text="NCCCCC([NH3+])C(=O)[O-]" />
+                    <has_text text="NC(CCCC[NH3+])C(=O)[O-]" />
+                    <has_text text="NCCCCC([NH3+])C(=O)O" />
+                    <has_text text="NC(CCCC[NH3+])C(=O)O" />
+                    <has_text text="NCCCCC(N)C(=O)O" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Dimorphite DL provides rules on how to enumerate the different charge forms of molecules using RDKit.
+Source code can be found here: https://git.durrantlab.pitt.edu/jdurrant/dimorphite_dl
+
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+- `SMILES Format`_
+
+.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+
+-----
+
+.. class:: infomark
+
+ **Output**
+
+SMILES format with the enumerated molecules. If an ID was provided in the input this is retained in the output.
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/s13321-019-0336-9</citation>
+        <citation type="bibtex">
+            @article{rdkit,
+            author = {Greg Landrum and others},
+            title = {RDKit: Open-source cheminformatics},
+            url ={http://www.rdkit.org}
+            }</citation>
+    </citations>
+</tool>