view filter/multi_obgrep.xml @ 0:6493d130f018

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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>


**What it does**

Providing a query file with SMARTS pattern in each line. These tool will run obgreg in parallel and merges the results.

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**Example**



    </help>
</tool>