Mercurial > repos > bgruening > osra
annotate osra.xml @ 2:d2490712b67d draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
| author | bgruening |
|---|---|
| date | Sun, 01 Nov 2015 10:35:04 -0500 |
| parents | 34ae5f2ae450 |
| children | aeb1f7daa7c2 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="ctb_osra" name="Molecule recognition" version="0.3"> |
| 2 <description>in Images or PDF documents (OSRA)</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.0.0">osra</requirement> | |
| 5 <requirement type="package" version="2.3.2">openbabel</requirement> | |
| 6 <requirement type="package" version="1.3.18">graphicsmagick</requirement> | |
| 7 </requirements> | |
| 8 <command interpreter='python'> | |
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d2490712b67d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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9 <![CDATA[ |
| 0 | 10 ## OSRA_DATA_FILES is set during the toolshed Installation |
| 11 ## if it is not set, use the standard configuration and hope the best | |
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d2490712b67d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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12 osra.py -f $oformat $infile |
| 0 | 13 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt |
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d2490712b67d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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14 |
| 0 | 15 ## further additions of OSRA parameter should go after -l and -a |
| 16 ## because -l and -a can be removed by the python wrapper | |
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d2490712b67d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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17 |
| 0 | 18 $confidence |
| 19 $adaptive | |
| 20 $thinning | |
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d2490712b67d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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21 |
| 0 | 22 > $outfile |
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d2490712b67d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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0
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23 ]]> |
| 0 | 24 </command> |
| 25 <inputs> | |
| 26 <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/> | |
| 27 <param name="oformat" type="select" label="Output molecule format"> | |
| 28 <option value="can">SMILES</option> | |
| 29 <option value="sdf">SDF</option> | |
| 30 </param> | |
| 31 <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" /> | |
| 32 <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images (-i)" truevalue="-i" falsevalue="" checked="false" /> | |
| 33 <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" /> | |
| 34 | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data name="outfile" type="data" format="sdf"> | |
| 38 <change_format> | |
| 39 <when input="oformat" value="can" format="smi"/> | |
| 40 </change_format> | |
| 41 </data> | |
| 42 </outputs> | |
| 43 <tests> | |
| 44 <test> | |
| 45 <param name="infile" ftype="png" value="CID_2244.png"/> | |
| 46 <param name="oformat" value="sdf"/> | |
| 47 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/> | |
| 48 </test> | |
| 49 <test> | |
| 50 <param name="infile" ftype="png" value="2008001635_153_chem.png"/> | |
| 51 <param name="oformat" value="can"/> | |
| 52 <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/> | |
| 53 </test> | |
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d2490712b67d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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54 |
| 0 | 55 </tests> |
| 56 <help> | |
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2
d2490712b67d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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0
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changeset
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57 <![CDATA[ |
| 0 | 58 |
| 59 .. class:: infomark | |
| 60 | |
| 61 **What this tool does** | |
| 62 | |
| 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. | |
| 64 | |
| 65 .. _OSRA: http://cactus.nci.nih.gov/osra/ | |
| 66 | |
| 67 ----- | |
| 68 | |
| 69 .. class:: infomark | |
| 70 | |
| 71 **Cite** | |
| 72 | |
| 73 Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_ | |
| 74 | |
| 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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d2490712b67d
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
76 ]]> |
| 0 | 77 </help> |
| 78 </tool> |