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ContentMine / phylotree

A repository for ami-phylotree development
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ami-phylo commandline #9

Open petermr opened 9 years ago

petermr commented 9 years ago

ami-phylo will run from the commandline and should, as far as possible, manage options from there. Please list here the options that should be part of the commandline.

petermr commented 9 years ago

output raw HOCR as SVG. (new issue opened)

petermr commented 9 years ago

Suggested commandline:

        String cmd = "--ph.phylo -q target/phylo/"+name+
                " -i image/"+img+".pbm.png"+
                " --hocr.html image/"+img+".hocr.html"+
                " --hocr.svg image/"+img+".hocr.svg"+
                " --ph.svg image/"+img+".svg"+
                " --ph.nwk image/"+img+".nwk"+
                " --ph.nexml image/"+img+".nexml.xml"+
                " --log image/"+img+".log.xml"+
                "";
        PhyloTreePlugin phyloPlugin = new PhyloTreePlugin(cmd);
        phyloPlugin.runAndOutput();

This should deal with most of what we want in and out of the calculation. Are there any input parameters that we also need to set?