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comparison osra.xml @ 5:b2edf498e8fb draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:39:51 -0400
parents aeb1f7daa7c2
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4:aeb1f7daa7c2 5:b2edf498e8fb
1 <tool id="ctb_osra" name="Molecule recognition" version="2.1.0"> 1 <tool id="ctb_osra" name="Molecule recognition" version="2.1.0">
2 <description>in Images or PDF documents (OSRA)</description> 2 <description>in PDF documents (OSRA)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1.0">osra</requirement> 4 <requirement type="package" version="2.1.0">osra</requirement>
5 <requirement type="package" version="0.52">poppler</requirement>
5 </requirements> 6 </requirements>
6 <command detect_errors="aggressive"> 7 <command detect_errors="aggressive">
7 <![CDATA[ 8 <![CDATA[
8 osra 9 osra
9 -f $oformat 10 -f $oformat
42 <test> 43 <test>
43 <param name="infile" value="CID_2244.pdf" ftype="pdf"/> 44 <param name="infile" value="CID_2244.pdf" ftype="pdf"/>
44 <param name="oformat" value="sdf"/> 45 <param name="oformat" value="sdf"/>
45 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/> 46 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/>
46 </test> 47 </test>
48 <!-- <test>
49 <param name="infile" value="CID_2244.png" ftype="png"/>
50 <param name="oformat" value="sdf"/>
51 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/>
52 </test> -->
47 <!--test> 53 <!--test>
48 PNGs producing a core-dump in osra 54 PNGs producing a core-dump in osra
49 <param name="infile" value="2008001635_153_chem.png"/> 55 <param name="infile" value="2008001635_153_chem.png"/>
50 <param name="oformat" value="can"/> 56 <param name="oformat" value="can"/>
51 <output name="outfile" ftype="smi" file="2008001635_153_chem.smi"/> 57 <output name="outfile" ftype="smi" file="2008001635_153_chem.smi"/>
56 62
57 .. class:: infomark 63 .. class:: infomark
58 64
59 **What this tool does** 65 **What this tool does**
60 66
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. 67 OSRA_ (Optical Structure Recognition Application) is a utility designed to convert graphical representations of chemical structures, contained within a PDF file, into a SMILES or SDF representation.
62 68
63 .. _OSRA: http://cactus.nci.nih.gov/osra/ 69 .. _OSRA: http://cactus.nci.nih.gov/osra/
64 70
65 .. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r 71 .. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r
66 ]]> 72 ]]>