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comparison osra.xml @ 2:d2490712b67d draft

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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
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1:0916781bc971 2:d2490712b67d
4 <requirement type="package" version="2.0.0">osra</requirement> 4 <requirement type="package" version="2.0.0">osra</requirement>
5 <requirement type="package" version="2.3.2">openbabel</requirement> 5 <requirement type="package" version="2.3.2">openbabel</requirement>
6 <requirement type="package" version="1.3.18">graphicsmagick</requirement> 6 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
7 </requirements> 7 </requirements>
8 <command interpreter='python'> 8 <command interpreter='python'>
9 <![CDATA[
9 ## OSRA_DATA_FILES is set during the toolshed Installation 10 ## OSRA_DATA_FILES is set during the toolshed Installation
10 ## if it is not set, use the standard configuration and hope the best 11 ## if it is not set, use the standard configuration and hope the best
11 osra.py -f $oformat $infile 12 osra.py -f $oformat $infile
12 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt 13 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
13 14
14 ## further additions of OSRA parameter should go after -l and -a 15 ## further additions of OSRA parameter should go after -l and -a
15 ## because -l and -a can be removed by the python wrapper 16 ## because -l and -a can be removed by the python wrapper
16 17
17 $confidence 18 $confidence
18 $adaptive 19 $adaptive
19 $thinning 20 $thinning
20 21
21 > $outfile 22 > $outfile
23 ]]>
22 </command> 24 </command>
23 <inputs> 25 <inputs>
24 <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/> 26 <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/>
25 <param name="oformat" type="select" label="Output molecule format"> 27 <param name="oformat" type="select" label="Output molecule format">
26 <option value="can">SMILES</option> 28 <option value="can">SMILES</option>
47 <test> 49 <test>
48 <param name="infile" ftype="png" value="2008001635_153_chem.png"/> 50 <param name="infile" ftype="png" value="2008001635_153_chem.png"/>
49 <param name="oformat" value="can"/> 51 <param name="oformat" value="can"/>
50 <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/> 52 <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/>
51 </test> 53 </test>
52 54
53 </tests> 55 </tests>
54 <help> 56 <help>
57 <![CDATA[
55 58
56 .. class:: infomark 59 .. class:: infomark
57 60
58 **What this tool does** 61 **What this tool does**
59 62
68 **Cite** 71 **Cite**
69 72
70 Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_ 73 Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_
71 74
72 .. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r 75 .. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r
76 ]]>
73 </help> 77 </help>
74 </tool> 78 </tool>