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Following a MatrixREDUCE or MotifREDUCE run, a bunch of output files (model parameters, PSAMs etc.) are generated. The HTMLSummary utility program is provided to summarize the main results in a intuitive, easy to follow HTML page so that (even non-expert) users can quickly make sense of their findings, e.g., the top list of significant PSAMs (motifs). Internally, HTMLSummary makes system-calls to the utility program LogoGenerator to create the logo images. These inter-connected programs, plus a few others, constitute the REDUCE Suite.

HTMLSummary [options] [-file=HTMLFile]

  Required parameters:

  Optional parameters:
    [-output=dir_name]  --- path to an MatrixREDUCE/MotifREDUCE run directory,
                            used both as input and output for HTML summary (./)
    [-copy]             --- copy CSS, JavsScript and associated image files to
                            the output directory to make the HTML self-contained
    [-rc]               --- logo based on reverse complementary strand
    [-width=ThumbnailImageWidthInPixel]   (145)
    [-height=ThumbnailImageHeightInPixel] (90)
    [-psam_list=list_of_PSAMs] --- generate a summary LOGO page for the list
                                   of PSAMs in the file
    [-file=HTMLFile]    --- HTML output file name (index.html)

  Usage: (following a MatrixREDUCE run)
    HTMLSummary -psam=psams.list -file=psams.html


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