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1 <tool id="osra" name="Molecule recognition" version="0.3">
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3
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2 <description>in Images or PDF documents (OSRA)</description>
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3 <requirements>
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4
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4 <requirement type="package" version="2.0.0">osra</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 ## OSRA_DATA_FILES is set during the toolshed Installation
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8 ## if it is not set, use the standard configuration and hope the best
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9 osra.py -f $oformat $infile
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10 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
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11
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12 ## further additions of OSRA parameter should go after -l and -a
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13 ## because -l and -a can be removed by the python wrapper
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14
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15 > $outfile
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16 </command>
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17 <inputs>
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18 <param format="png,pdf" label="Image or PDF with molecules" name="infile" type="data" />
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19 <param label="Output molecule format" name="oformat" type="select">
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20 <option value="can">SMILES</option>
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21 <option value="sdf">SDF</option>
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data format="sdf" name="outfile" type="data">
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26 <change_format>
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27 <when format="smi" input="oformat" value="can" />
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28 </change_format>
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29 </data>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param ftype="png" name="infile" value="CID_2244.png" />
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34 <param name="oformat" value="sdf" />
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35 <output file="osra_on_CID2244.sdf" ftype="sdf" name="outfile" />
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36 </test>
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37 </tests>
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38 <help>
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39
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40 **What it does**
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41
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42 OSRA detects molecules in images and converts them to standard molecule formats.
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43
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44
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45 </help>
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46 </tool>
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