details: http://www.bx.psu.edu/hg/galaxy/rev/6041065f86a9 changeset: 1650:6041065f86a9 user: Dan Blankenberg <dan@bx.psu.edu> date: Thu Dec 04 15:09:57 2008 -0500 description: Update GMAJ help. 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (33 lines): diff -r 8b9cd2a1d5c2 -r 6041065f86a9 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Thu Dec 04 11:40:42 2008 -0500 +++ b/tools/visualization/GMAJ.xml Thu Dec 04 15:09:57 2008 -0500 @@ -176,13 +176,25 @@ <data name="out_file1" format="gmaj.zip"/> </outputs> <help> -You can use this tool to view a set of MAF alignments. You may also include optional annotation data for one or more of the organisms. +.. class:: infomark + +**Reference Sequence:** +The default option, "First sequence in each block", is the correct choice for the vast majority of MAF alignments. The alternative, "Any sequence", will allow you to flip the blocks to view them with any of the MAF sequences as the reference, but this is only appropriate if the file was generated by a sequence-symmetric alignment program such as TBA_. Using "Any sequence" with an ordinary MAF will **not** give the same results as if that alignment had been run with a different reference sequence. + +.. class:: infomark + +**Annotation Style:** +The default style, "Galaxy", specifies one set of annotations for each species in the MAF file; it assumes that if you have, say, exons for several chromosomes of one species, they are all together in one file. The other style, "Basic", is more flexible but cumbersome: a separate set of files is specified for each sequence (e.g. chromosome), and you must fill in the full sequence name as it appears in the MAF. The Basic style also allows you to provide a display offset that GMAJ will add to all of the position labels for that sequence. With either style, specifying more than one set of annotations for the same sequence will result in an error message from GMAJ. + +---- + +**What it does** + +GMAJ is an interactive viewer for MAF alignments, with support for optional annotation data. In addition to browsing the alignments, you can select and export them according to a variety of criteria and send the output back to your Galaxy history. For detailed information on GMAJ, click here_. .. _here: /static/gmaj/docs/gmaj_readme.html - -Gmaj is a tool for viewing and manipulating Generalized Multiple Alignments (GMAs) produced by programs such as TBA (though it can also be used with maf-format alignments from other sources). It can display interactive graphical and text representations of the alignments, a diagram showing the locations of exons and repeats, and other annotations -- all with the user's choice of reference sequence. - +.. _TBA: http://www.bx.psu.edu/miller_lab/ </help> </tool>