diff subsearch/subsearch.xml @ 0:527ecd2fc500 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/subsearch/subsearch.xml	Thu Aug 15 03:25:06 2013 -0400
@@ -0,0 +1,73 @@
+<tool id="ctb_subsearch" name="Substructure Search" version="0.1">
+    <description>of fingerprint data sets</description>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter="python">
+
+    subsearch.py
+        -i $query
+        --iformat "${query.ext}"
+        --fastsearch-index "${os.path.join($fastsearch.extra_files_path,'molecule.fs')}"
+        -o "${outfile}"
+        --oformat $oformat
+        --max-candidates $max_candidates
+        --processors 10
+
+    </command>
+    <inputs>
+        <param name="query" type='data' format="tabular,smi,sdf,inchi,text" label="query"/>
+        <param name="fastsearch" type='data' format="obfs" label="OpenBabel Fastsearch Index"/>
+        <param name="max_candidates" size="6" type="integer" value="4000" label="The maximum number of candidates"/>
+        <param name='oformat' type='select' format='text' label="Output format.">
+            <option value='smi'>SMILES</option>
+            <option value='inchi'>InChI</option>
+            <option value='sdf'>SD-Files</option>
+            <option value='mol2'>mol2</option>
+            <option value='names'>Return the molecule names only</option>
+        </param>
+    </inputs>
+    <outputs>
+       <data format="smi" name="outfile">
+         <change_format>
+           <when input="oformat" value="inchi" format="inchi"/>
+           <when input="oformat" value="sdf" format="sdf"/>
+           <when input="oformat" value="mol2" format="mol2"/>
+           <when input="oformat" value="names" format="tabular"/>
+         </change_format>
+       </data>
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Substructure search in based on Open Babel FastSearch_ Index. It uses molecular fingerprints to prepare and search an index of a multi-molecule datafile.
+
+.. _FastSearch: http://openbabel.org/wiki/FastSearch
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+SMILES or SMARTS patterns are possible. SD- and InChI files are converted to SMILES.
+
+-----
+
+.. class:: infomark
+
+**Cite**
+
+`Open Babel`_
+
+.. _Open Babel: http://openbabel.org/wiki/Main_Page
+
+    </help>
+</tool>