diff modify/remove_protonation_state.xml @ 0:527ecd2fc500 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/modify/remove_protonation_state.xml	Thu Aug 15 03:25:06 2013 -0400
@@ -0,0 +1,43 @@
+<tool id="ctb_remove_protonation_state" name="Remove protonation state" version="0.1">
+    <description>of every atom</description>
+    <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter='python'>
+    remove_protonation_state.py
+        -i $infile
+        -o $outfile
+        --iformat "${infile.ext}"
+        2>&#38;1
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="sdf,smi,mol,inchi" label="Molecule file" help="Dataset missing? See TIP below"/>
+    </inputs>
+    <outputs>
+        <data format_source="infile" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Removes the protonation state of every atom.
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+`Open Babel`_
+
+.. _Open Babel: http://openbabel.org/wiki/Main_Page
+
+    </help>
+</tool>