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comparison osra.xml @ 11:143a63ca2bca

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author bgruening
date Thu, 23 May 2013 16:19:16 -0400
parents deccc074dbfb
children ab9e2350406b
comparison
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10:dcbe4666c052 11:143a63ca2bca
1 <tool id="osra" name="Molecule recognition" version="0.2"> 1 <tool id="osra" name="Molecule recognition" version="0.3">
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="1.4.0">osra</requirement> 4 <requirement type="package" version="2.0.0">osra</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter='python'> 6 <command interpreter='python'>
7 ## OSRA_DATA_FILES is set during the toolshed Installation 7 ## OSRA_DATA_FILES is set during the toolshed Installation
8 ## if it is not set, use the standard configuration and hope the best 8 ## if it is not set, use the standard configuration and hope the best
9 osra.py -f $oformat $infile 9 osra.py -f $oformat $infile
10 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt 10 -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt
11 11
12 ## further additions of OSRA parameter should go after -l and -a 12 ## further additions of OSRA parameter should go after -l and -a
13 ## because -l and -a can be removed by the python wrapper 13 ## because -l and -a can be removed by the python wrapper
14 14
15 $confidence
16 $adaptive
17 $thinning
18
15 > $outfile 19 > $outfile
16 </command> 20 </command>
17 <inputs> 21 <inputs>
18 <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/> 22 <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/>
19 <param name="oformat" type="select" label="Output molecule format"> 23 <param name="oformat" type="select" label="Output molecule format">
20 <option value="can">SMILES</option> 24 <option value="can">SMILES</option>
21 <option value="sdf">SDF</option> 25 <option value="sdf">SDF</option>
22 </param> 26 </param>
27 <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" />
28 <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images (-i)" truevalue="-i" falsevalue="" checked="false" />
29 <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" />
30
23 </inputs> 31 </inputs>
24 <outputs> 32 <outputs>
25 <data name="outfile" type="data" format="sdf"> 33 <data name="outfile" type="data" format="sdf">
26 <change_format> 34 <change_format>
27 <when input="oformat" value="can" format="smi"/> 35 <when input="oformat" value="can" format="smi"/>
32 <test> 40 <test>
33 <param name="infile" ftype="png" value="CID_2244.png"/> 41 <param name="infile" ftype="png" value="CID_2244.png"/>
34 <param name="oformat" value="sdf"/> 42 <param name="oformat" value="sdf"/>
35 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/> 43 <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/>
36 </test> 44 </test>
45 <test>
46 <param name="infile" ftype="png" value="2008001635_153_chem.png"/>
47 <param name="oformat" value="can"/>
48 <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/>
49 </test>
50
37 </tests> 51 </tests>
38 <help> 52 <help>
39 53
40 **What it does** 54 **What it does**
41 55