Mercurial > repos > bgruening > osra
comparison osra.xml @ 4:aeb1f7daa7c2 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
author | bgruening |
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date | Thu, 09 Nov 2017 03:41:42 -0500 |
parents | d2490712b67d |
children | b2edf498e8fb |
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3:e44dda38e6ae | 4:aeb1f7daa7c2 |
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1 <tool id="ctb_osra" name="Molecule recognition" version="0.3"> | 1 <tool id="ctb_osra" name="Molecule recognition" version="2.1.0"> |
2 <description>in Images or PDF documents (OSRA)</description> | 2 <description>in Images or PDF documents (OSRA)</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="2.0.0">osra</requirement> | 4 <requirement type="package" version="2.1.0">osra</requirement> |
5 <requirement type="package" version="2.3.2">openbabel</requirement> | |
6 <requirement type="package" version="1.3.18">graphicsmagick</requirement> | |
7 </requirements> | 5 </requirements> |
8 <command interpreter='python'> | 6 <command detect_errors="aggressive"> |
9 <![CDATA[ | 7 <![CDATA[ |
10 ## OSRA_DATA_FILES is set during the toolshed Installation | 8 osra |
11 ## if it is not set, use the standard configuration and hope the best | 9 -f $oformat |
12 osra.py -f $oformat $infile | 10 '$infile' |
13 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt | 11 -l `which osra | xargs dirname`/../share/spelling.txt |
12 -a `which osra | xargs dirname`/../share/superatom.txt | |
14 | 13 |
15 ## further additions of OSRA parameter should go after -l and -a | 14 $confidence |
16 ## because -l and -a can be removed by the python wrapper | 15 $adaptive |
17 | 16 $thinning |
18 $confidence | 17 > '$outfile' |
19 $adaptive | |
20 $thinning | |
21 | |
22 > $outfile | |
23 ]]> | 18 ]]> |
24 </command> | 19 </command> |
25 <inputs> | 20 <inputs> |
26 <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/> | 21 <param name="infile" type="data" format="pdf" label="PDF with molecules"/> |
27 <param name="oformat" type="select" label="Output molecule format"> | 22 <param name="oformat" type="select" label="Output molecule format"> |
28 <option value="can">SMILES</option> | 23 <option value="can">SMILES</option> |
29 <option value="sdf">SDF</option> | 24 <option value="sdf">SDF</option> |
30 </param> | 25 </param> |
31 <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" /> | 26 <param name="confidence" type="boolean" label="Print out confidence estimate" help=" (-p)" |
32 <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images (-i)" truevalue="-i" falsevalue="" checked="false" /> | 27 truevalue="-p" falsevalue="" checked="true" /> |
33 <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" /> | 28 <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images" help="(-i)" |
29 truevalue="-i" falsevalue="" checked="false" /> | |
30 <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents" help="(-j)" | |
31 truevalue="-j" falsevalue="" checked="false" /> | |
34 | 32 |
35 </inputs> | 33 </inputs> |
36 <outputs> | 34 <outputs> |
37 <data name="outfile" type="data" format="sdf"> | 35 <data name="outfile" format="sdf"> |
38 <change_format> | 36 <change_format> |
39 <when input="oformat" value="can" format="smi"/> | 37 <when input="oformat" value="can" format="smi"/> |
40 </change_format> | 38 </change_format> |
41 </data> | 39 </data> |
42 </outputs> | 40 </outputs> |
43 <tests> | 41 <tests> |
44 <test> | 42 <test> |
45 <param name="infile" ftype="png" value="CID_2244.png"/> | 43 <param name="infile" value="CID_2244.pdf" ftype="pdf"/> |
46 <param name="oformat" value="sdf"/> | 44 <param name="oformat" value="sdf"/> |
47 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/> | 45 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/> |
48 </test> | 46 </test> |
49 <test> | 47 <!--test> |
50 <param name="infile" ftype="png" value="2008001635_153_chem.png"/> | 48 PNGs producing a core-dump in osra |
49 <param name="infile" value="2008001635_153_chem.png"/> | |
51 <param name="oformat" value="can"/> | 50 <param name="oformat" value="can"/> |
52 <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/> | 51 <output name="outfile" ftype="smi" file="2008001635_153_chem.smi"/> |
53 </test> | 52 </test--> |
54 | |
55 </tests> | 53 </tests> |
56 <help> | 54 <help> |
57 <![CDATA[ | 55 <![CDATA[ |
58 | 56 |
59 .. class:: infomark | 57 .. class:: infomark |
62 | 60 |
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. | 61 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 | 62 |
65 .. _OSRA: http://cactus.nci.nih.gov/osra/ | 63 .. _OSRA: http://cactus.nci.nih.gov/osra/ |
66 | 64 |
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 | 65 .. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r |
76 ]]> | 66 ]]> |
77 </help> | 67 </help> |
68 <citations> | |
69 <citation type="bibtex"> | |
70 @inproceedings{filippov2010improvements, | |
71 title={Improvements in Optical Structure Recognition Application}, | |
72 author={Filippov, Igor V and Nicklaus, Marc C and Kinney, John}, | |
73 booktitle={Document Analysis Systems Workshop}, | |
74 year={2010} | |
75 } | |
76 </citation> | |
77 </citations> | |
78 </tool> | 78 </tool> |