Mercurial > repos > bgruening > osra
diff osra.xml @ 4:aeb1f7daa7c2 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/osra commit 74daed54894d9769a251a2ca6a46d96b7a27e461
author | bgruening |
---|---|
date | Thu, 09 Nov 2017 03:41:42 -0500 |
parents | d2490712b67d |
children | b2edf498e8fb |
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--- a/osra.xml Tue Mar 01 10:41:20 2016 -0500 +++ b/osra.xml Thu Nov 09 03:41:42 2017 -0500 @@ -1,40 +1,38 @@ -<tool id="ctb_osra" name="Molecule recognition" version="0.3"> +<tool id="ctb_osra" name="Molecule recognition" version="2.1.0"> <description>in Images or PDF documents (OSRA)</description> <requirements> - <requirement type="package" version="2.0.0">osra</requirement> - <requirement type="package" version="2.3.2">openbabel</requirement> - <requirement type="package" version="1.3.18">graphicsmagick</requirement> + <requirement type="package" version="2.1.0">osra</requirement> </requirements> - <command interpreter='python'> + <command detect_errors="aggressive"> <![CDATA[ - ## OSRA_DATA_FILES is set during the toolshed Installation - ## if it is not set, use the standard configuration and hope the best - osra.py -f $oformat $infile - -l \$OSRA_DATA_FILES/spelling.txt -a \$OSRA_DATA_FILES/superatom.txt +osra + -f $oformat + '$infile' + -l `which osra | xargs dirname`/../share/spelling.txt + -a `which osra | xargs dirname`/../share/superatom.txt - ## further additions of OSRA parameter should go after -l and -a - ## because -l and -a can be removed by the python wrapper - - $confidence - $adaptive - $thinning - - > $outfile + $confidence + $adaptive + $thinning + > '$outfile' ]]> </command> <inputs> - <param name="infile" type="data" format="png,pdf" label="Image or PDF with molecules"/> + <param name="infile" type="data" format="pdf" label="PDF with molecules"/> <param name="oformat" type="select" label="Output molecule format"> <option value="can">SMILES</option> <option value="sdf">SDF</option> </param> - <param name="confidence" type="boolean" label="Print out confidence estimate (-p)" truevalue="-p" falsevalue="" checked="true" /> - <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images (-i)" truevalue="-i" falsevalue="" checked="false" /> - <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents (-j)" truevalue="-j" falsevalue="" checked="false" /> + <param name="confidence" type="boolean" label="Print out confidence estimate" help=" (-p)" + truevalue="-p" falsevalue="" checked="true" /> + <param name="adaptive" type="boolean" label="Adaptive thresholding pre-processing, useful for low light/low contrast images" help="(-i)" + truevalue="-i" falsevalue="" checked="false" /> + <param name="thinning" type="boolean" label="Additional thinning/scaling down of low quality documents" help="(-j)" + truevalue="-j" falsevalue="" checked="false" /> </inputs> <outputs> - <data name="outfile" type="data" format="sdf"> + <data name="outfile" format="sdf"> <change_format> <when input="oformat" value="can" format="smi"/> </change_format> @@ -42,16 +40,16 @@ </outputs> <tests> <test> - <param name="infile" ftype="png" value="CID_2244.png"/> + <param name="infile" value="CID_2244.pdf" ftype="pdf"/> <param name="oformat" value="sdf"/> <output name="outfile" ftype="sdf" file="osra_on_CID2244.sdf"/> </test> - <test> - <param name="infile" ftype="png" value="2008001635_153_chem.png"/> + <!--test> + PNGs producing a core-dump in osra + <param name="infile" value="2008001635_153_chem.png"/> <param name="oformat" value="can"/> - <output name="outfile" ftype="sdf" file="2008001635_153_chem.smi"/> - </test> - + <output name="outfile" ftype="smi" file="2008001635_153_chem.smi"/> + </test--> </tests> <help> <![CDATA[ @@ -64,15 +62,17 @@ .. _OSRA: http://cactus.nci.nih.gov/osra/ ------ - -.. class:: infomark - -**Cite** - -Igor V Filippov and Marc C Nicklaus - `Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`_ - .. _`Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution`: http://pubs.acs.org/doi/abs/10.1021/ci800067r ]]> </help> + <citations> + <citation type="bibtex"> + @inproceedings{filippov2010improvements, + title={Improvements in Optical Structure Recognition Application}, + author={Filippov, Igor V and Nicklaus, Marc C and Kinney, John}, + booktitle={Document Analysis Systems Workshop}, + year={2010} + } + </citation> + </citations> </tool>