diff ob_remDuplicates.xml @ 0:75d6c2b7907a draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ob_remDuplicates.xml	Sat May 20 08:39:17 2017 -0400
@@ -0,0 +1,78 @@
+<tool id="openbabel_remDuplicates" name="Remove duplicated molecules" version="@VERSION@.0">
+    <description></description>
+    <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism-->
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive">
+<![CDATA[
+    obabel
+      -i"${infile.ext}"
+       "${infile}"
+      -ocopy
+      --unique "${descriptor}"
+      -O "${outfile}"
+      -e
+]]>
+    </command>
+    <inputs>
+        <expand macro="infile_all_types"/>
+        <param name="descriptor" type="select" label="Select descriptor for molecule comparison">
+            <option value="inchi" selected="True">InChI (default)</option>
+            <option value="cansmi">Canonical SMILES</option>
+            <option value="cansmiNS">Canonical SMILES (without stereo)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="output_like_input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="smi" value="2_mol.smi"/>
+                <param name="descriptor" value="inchi" />
+            <output name="outfile" ftype="smi" file="ob_remDuplicates_on_2_mol.smi" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+Filters a library of compounds and removes duplicated molecules.
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+Comparison based on Canonical SMILES without stereochemistry may be useful in cases where this information is not crucial for library preparation. Several VS tools will automatically generate stereoisomeric forms.
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+| - `InChI`_
+| - `SMILES Format`_
+
+.. _InChI: http://www.iupac.org/home/publications/e-resources/inchi.html
+.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+Same as input format.
+
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>