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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter/multi_obgrep.xml	Thu Aug 15 03:25:06 2013 -0400
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+<tool id="ctb_multi_obgrep" name="Multi Compound Search" version="0.1">
+    <description>an advanced molecular grep program using SMARTS</description>
+    <requirements>
+        <requirement type="package" version="2.3.2">openbabel</requirement>
+    </requirements>
+    <command interpreter="python">
+
+    multi_obgrep.py
+        -i $infile
+        --iformat ${infile.ext}
+        -q $query
+        -o "${outfile}"
+        $invert_matches
+        --n-times $n_times
+        $only_name
+        $full_match
+        $number_of_matches
+        --processors 10
+
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="sdf,mol,mol2,cml,inchi,smi" label="Compound File" help="Specify a compound file in SDF Format"/>
+        <param name="query" type='data' format="tabular,text" label="Query file" help="One SMARTS pattern in each line."/>
+        <param name="invert_matches" type="boolean" label="Invert the matching, print non-matching molecules (-v)" truevalue="--invert-matches" falsevalue="" checked="false" />
+        <param name="n_times" type="integer" value="0" label="Print a molecule only if the pattern occurs # times inside the molecule" />
+        <param name="only_name" type="boolean" label="Only print the name of the molecules (-n)" truevalue="--only-name" falsevalue="" checked="false" />
+        <param name="full_match" type="boolean" label="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern (-f)" truevalue="--full-match" falsevalue="" checked="false" />
+        <param name="number_of_matches" type="boolean" label="Print the number of matches (-c)" truevalue="--number-of-matches" falsevalue="" checked="false" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format_source="infile" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+
+.. class:: infomark
+
+**What this tool does**
+
+Uses the Open Babel Obgrep_ to search for molecules inside multi-molecule files (e.g. SMI, SDF, etc.) or across multiple files.
+It is known that not all SMARTS features from the Daylight Toolkit are supported, please have a look here_.
+
+.. _Obgrep: http://openbabel.org/wiki/Obgrep
+.. _here: http://openbabel.org/wiki/SMARTS
+
+-----
+
+.. class:: infomark
+
+**Input**
+
+| - `SD-Format`_
+| - `SMILES Format`_
+
+.. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
+.. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
+
+-----
+
+.. 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>