Mercurial > repos > bgruening > osra

comparison osra.xml @ 0:34ae5f2ae450 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Thu, 15 Aug 2013 03:30:25 -0400
parents
children d2490712b67d
comparison
equal deleted inserted replaced
-1:000000000000 0:34ae5f2ae450
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'>
9 ## OSRA_DATA_FILES is set during the toolshed Installation
10 ## if it is not set, use the standard configuration and hope the best
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
17 $confidence
18 $adaptive
19 $thinning
20
21 > $outfile
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>
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
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>
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
53 </tests>
54 <help>
55
56 .. class:: infomark
57
58 **What this tool does**
59
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.
61
62 .. _OSRA: http://cactus.nci.nih.gov/osra/
63
64 -----
65
66 .. class:: infomark
67
68 **Cite**
69
70 Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_
71
72 .. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r
73 </help>
74 </tool>