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annotate osra.xml @ 20:4f0d88f40ea1 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
author bgruening
date Sun, 01 Nov 2015 10:34:50 -0500
parents b8c0edfefc91
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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 <![CDATA[
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10 ## OSRA_DATA_FILES is set during the toolshed Installation
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11 ## if it is not set, use the standard configuration and hope the best
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12 osra.py -f $oformat $infile
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13 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
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15 ## further additions of OSRA parameter should go after -l and -a
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16 ## because -l and -a can be removed by the python wrapper
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18 $confidence
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19 $adaptive
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20 $thinning
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22 > $outfile
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/>
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27 <param name="oformat" type="select" label="Output molecule format">
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28 <option value="can">SMILES</option>
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29 <option value="sdf">SDF</option>
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30 </param>
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31 <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" />
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32 <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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33 <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" />
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34
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35 </inputs>
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36 <outputs>
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37 <data name="outfile" type="data" format="sdf">
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38 <change_format>
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39 <when input="oformat" value="can" format="smi"/>
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40 </change_format>
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41 </data>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="infile" ftype="png" value="CID_2244.png"/>
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46 <param name="oformat" value="sdf"/>
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47 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/>
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48 </test>
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49 <test>
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50 <param name="infile" ftype="png" value="2008001635_153_chem.png"/>
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51 <param name="oformat" value="can"/>
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52 <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/>
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53 </test>
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54
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55 </tests>
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56 <help>
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57 <![CDATA[
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59 .. class:: infomark
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60
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61 **What this tool does**
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63 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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64
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65 .. _OSRA: http://cactus.nci.nih.gov/osra/
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67 -----
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69 .. class:: infomark
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71 **Cite**
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73 Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_
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75 .. _`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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76 ]]>
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77 </help>
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78 </tool>