view osra.xml @ 16:200638e19f51

test

<tool id="osra" name="Molecule recognition" version="0.3">
    <description>in Images or PDF documents (OSRA)</description>
    <requirements>
        <requirement type="package" version="2.0.0">osra</requirement>
    </requirements>
    <command interpreter="python">
        ## OSRA_DATA_FILES is set during the toolshed Installation
        ## if it is not set, use the standard configuration and hope the best
        osra.py -f $oformat $infile 
        -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
        
        ## further additions of OSRA parameter should go after -l and -a
        ## because -l and -a can be removed by the python wrapper
        
        &gt; $outfile
    </command>
    <inputs>
        <param format="png,pdf" label="Image or PDF with molecules" name="infile" type="data" />
        <param label="Output molecule format" name="oformat" type="select">
            <option value="can">SMILES</option>
            <option value="sdf">SDF</option>
        </param>
    </inputs>
    <outputs>
        <data format="sdf" name="outfile" type="data">
            <change_format>
                <when format="smi" input="oformat" value="can" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param ftype="png" name="infile" value="CID_2244.png" />
            <param name="oformat" value="sdf" />
            <output file="osra_on_CID2244.sdf" ftype="sdf" name="outfile" />
        </test>
    </tests>
    <help>

**What it does**

OSRA detects molecules in images and converts them to standard molecule formats. 


    </help>
</tool>