diff filter/ob_remIons.xml @ 0:527ecd2fc500 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter/ob_remIons.xml	Thu Aug 15 03:25:06 2013 -0400
@@ -0,0 +1,62 @@
+<tool id="ctb_remIons" name="Remove counterions and fragments" version="1.0">
+    <description></description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="50000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter="python">
+    ob_remIons.py
+      -i "${infile}"
+      -iformat "${infile.ext}"
+      -o "${outfile}"
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Select input file with multiple molecules"/>
+    </inputs>
+    <outputs>
+        <data format_source="infile" name="outfile"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="smi" value="2_mol.smi"/>
+            <output name="outfile" ftype="smi" file="obrmions_on_2_mol.smi" />
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Parses a multiple molecules file and deletes any present counterions or fragments.
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+| Only the **largest fragment** on every molecule is extracted.
+| 
+| Only molecules with more than 5 heavy atoms are parsed.
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+N M O'Boyle, C Morley and G R Hutchison - `Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`_
+
+.. _`Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit`: http://journal.chemistrycentral.com/content/2/1/5
+
+N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison - `Open Babel: An open chemical toolbox.`_
+
+.. _`Open Babel: An open chemical toolbox.`: http://www.jcheminf.com/content/3/1/33
+
+`Open Babel`_
+
+.. _`Open Babel`: http://openbabel.org/wiki/Main_Page
+
+    </help>
+</tool>