view osra.xml @ 8:dfa05117e30a

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<tool id="osra" name="Molecule recognition" version="0.2">
    <description>in Images or PDF documents (OSRA)</description>
    <requirements>
        <requirement type="package" version="1.4.0">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
        
        > $outfile
    </command>
    <inputs>
        <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/>
        <param name="oformat" type="select" label="Output molecule format">
            <option value="can">SMILES</option>
            <option value="sdf">SDF</option>
        </param>
    </inputs>
    <outputs>
        <data name="outfile" type="data" format="sdf">
            <change_format>
                <when input="oformat" value="can" format="smi"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="infile" ftype="png" value="CID_2244.png"/>
            <param name="oformat" value="sdf"/>
            <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/>
        </test>
    </tests>
    <help>

**What it does**

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


    </help>
</tool>