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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter/ob_remSmall.xml	Thu Aug 15 03:25:06 2013 -0400
@@ -0,0 +1,70 @@
+<tool id="ctb_remSmall" name="Remove small molecules" version="1.0">
+    <description></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>
+    obabel
+      -i"${infile.ext}"
+      "${infile}"
+      -ocopy
+      -O "${outfile}"
+      --filter "atoms > $cutoff"
+      -e
+      2>&#38;1
+    </command>
+    <inputs>
+        <param name="infile" format="sdf,mol,mol2,cml,inchi,smi" type="data" label="Molecular input file" />
+        <param name="cutoff" size="3" type="integer" value="5" label="Specify the cut-off value (only molecules with more than this number of atoms will pass the filter)" />
+    </inputs>
+    <outputs>
+        <data format_source="infile" name="outfile" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" ftype="smi" value="3_mol.smi" />
+            <param name="cutoff" value="5" />
+            <output name="outfile" ftype="smi" file="obremsmall_on_3_mol.smi" />
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Filters a library of compounds and removes small molecules below a predefined input number of atoms.
+
+-----
+
+.. class:: warningmark
+
+**Hint**
+
+Some libraries may contain molecules without a 1D/3D descriptor. These molecules may provoke crashes of any other tool. It is strongly adviced to run this tool before proceeding to any further steps.
+
+-----
+
+.. class:: infomark
+
+**Output**
+
+Same as input format.
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+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>