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1 <tool id="ctb_osra" name="Molecule recognition" version="0.3">
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2 <description>in Images or PDF documents (OSRA)</description>
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3 <requirements>
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4 <requirement type="package" version="2.0.0">osra</requirement>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
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7 </requirements>
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8 <command interpreter='python'>
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9 ## OSRA_DATA_FILES is set during the toolshed Installation
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10 ## if it is not set, use the standard configuration and hope the best
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11 osra.py -f $oformat $infile
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12 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
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13
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14 ## further additions of OSRA parameter should go after -l and -a
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15 ## because -l and -a can be removed by the python wrapper
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16
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17 $confidence
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18 $adaptive
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19 $thinning
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20
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21 > $outfile
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22 </command>
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23 <inputs>
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24 <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/>
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25 <param name="oformat" type="select" label="Output molecule format">
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26 <option value="can">SMILES</option>
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27 <option value="sdf">SDF</option>
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28 </param>
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29 <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" />
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30 <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images (-i)" truevalue="-i" falsevalue="" checked="false" />
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31 <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" />
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32
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33 </inputs>
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34 <outputs>
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35 <data name="outfile" type="data" format="sdf">
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36 <change_format>
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37 <when input="oformat" value="can" format="smi"/>
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38 </change_format>
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39 </data>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name="infile" ftype="png" value="CID_2244.png"/>
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44 <param name="oformat" value="sdf"/>
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45 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/>
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46 </test>
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47 <test>
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48 <param name="infile" ftype="png" value="2008001635_153_chem.png"/>
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49 <param name="oformat" value="can"/>
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50 <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/>
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51 </test>
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52
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53 </tests>
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54 <help>
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55
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56 .. class:: infomark
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57
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58 **What this tool does**
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59
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60 OSRA_ (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures into SMILES or SDF. It generates the SMILES or SDF representation of any molecular structure image within a document which is parseable by GraphicMagick.
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61
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62 .. _OSRA: http://cactus.nci.nih.gov/osra/
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63
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64 -----
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65
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66 .. class:: infomark
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67
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68 **Cite**
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69
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70 Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_
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71
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72 .. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r
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73 </help>
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74 </tool>
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