Mercurial > repos > bgruening > osra
annotate osra.xml @ 17:b8c0edfefc91
ChemicalToolBoX update.
| author | Bjoern Gruening <bjoern.gruening@gmail.com> |
|---|---|
| date | Fri, 19 Jul 2013 16:28:14 +0200 |
| parents | d97d51e9bb95 |
| children | 4f0d88f40ea1 |
| rev | line source |
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d97d51e9bb95
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
13
diff
changeset
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1 <tool id="ctb_osra" name="Molecule recognition" version="0.3"> |
| 3 | 2 <description>in Images or PDF documents (OSRA)</description> |
| 0 | 3 <requirements> |
| 11 | 4 <requirement type="package" version="2.0.0">osra</requirement> |
| 13 | 5 <requirement type="package" version="2.3.2">openbabel</requirement> |
| 6 <requirement type="package" version="1.3.18">graphicsmagick</requirement> | |
| 0 | 7 </requirements> |
| 3 | 8 <command interpreter='python'> |
| 2 | 9 ## OSRA_DATA_FILES is set during the toolshed Installation |
| 10 ## if it is not set, use the standard configuration and hope the best | |
| 3 | 11 osra.py -f $oformat $infile |
| 12 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt | |
| 13 | |
| 14 ## further additions of OSRA parameter should go after -l and -a | |
| 15 ## because -l and -a can be removed by the python wrapper | |
| 16 | |
| 11 | 17 $confidence |
| 18 $adaptive | |
| 19 $thinning | |
| 20 | |
| 2 | 21 > $outfile |
| 0 | 22 </command> |
| 23 <inputs> | |
| 24 <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/> | |
| 25 <param name="oformat" type="select" label="Output molecule format"> | |
| 26 <option value="can">SMILES</option> | |
| 27 <option value="sdf">SDF</option> | |
| 28 </param> | |
| 11 | 29 <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" /> |
| 30 <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images (-i)" truevalue="-i" falsevalue="" checked="false" /> | |
| 31 <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" /> | |
| 32 | |
| 0 | 33 </inputs> |
| 34 <outputs> | |
| 35 <data name="outfile" type="data" format="sdf"> | |
| 36 <change_format> | |
| 37 <when input="oformat" value="can" format="smi"/> | |
| 38 </change_format> | |
| 39 </data> | |
| 40 </outputs> | |
| 41 <tests> | |
| 42 <test> | |
| 43 <param name="infile" ftype="png" value="CID_2244.png"/> | |
| 44 <param name="oformat" value="sdf"/> | |
| 45 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/> | |
| 46 </test> | |
| 11 | 47 <test> |
| 48 <param name="infile" ftype="png" value="2008001635_153_chem.png"/> | |
| 49 <param name="oformat" value="can"/> | |
| 50 <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/> | |
| 51 </test> | |
| 52 | |
| 0 | 53 </tests> |
| 54 <help> | |
| 55 | |
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17
b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
56 .. class:: infomark |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
57 |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
58 **What this tool does** |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
59 |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
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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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
61 |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
62 .. _OSRA: http://cactus.nci.nih.gov/osra/ |
| 0 | 63 |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
64 ----- |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
65 |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
66 .. class:: infomark |
| 0 | 67 |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
68 **Cite** |
| 0 | 69 |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
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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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
71 |
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b8c0edfefc91
ChemicalToolBoX update.
Bjoern Gruening <bjoern.gruening@gmail.com>
parents:
16
diff
changeset
|
72 .. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r |
| 0 | 73 </help> |
| 74 </tool> |